Reference
If you use the results of PHASTER, please cite the following:
Arndt, D., Grant, J., Marcu, A., Sajed, T., Pon, A., Liang, Y., Wishart, D.S. (2016) "PHASTER: a better, faster version of the PHAST phage search tool", Nucleic Acids Research (submitted).
Reference Tables and Figures
Quick Links
Table 1: PHASTER’s performance upgradesTable 2: Feature comparison between PHAST and PHASTER
Figure 1: Contig length and sensitivity
Table 3: PHASTER evaluation (summary)
Table 4: PHASTER evaluation on GenBank annotated genomes
Table 5: PHASTER evaluation on unannotated genomes
Table 1: Details of PHASTER’s performance upgrades, and a comparison of their impact on runtimes for a 5.5 Mbp test genome (Escherichia coli O157:H7,GenBank accession NC_002655)
| Cumulative set of performance enhancements | BLAST vs. viral DB runtime (s) | BLAST vs. bacterial DB runtime (s) | Total runtime on GenBank annotated genome (s) | Total runtime on unannotated genome (s) |
|---|---|---|---|---|
| PHAST (baseline) current DBs, no other upgrades | 191 | 576 | 270 | 899 |
| PHASTER (upgrade 1) - filter bacterial DB | 191 | 309 | 270 | 632 |
| PHASTER (upgrade 2) - cluster upgrade | 88 | 166 | 167 | 386 |
| PHASTER (upgrade 3) - BLAST+ | 77 | 132 | 156 | 341 |
| PHASTER (upgrade 4) - partition query sequences evenly | 47 | 103 | 126 | 282 |
| PHASTER (upgrade 5) - bacterial DB, optimize parameters | 47 | 48 | 126 | 227 |
| PHASTER (upgrade 6) - faster front-end server | 47 | 48 | 100 | 205 |
Table 2: A feature comparison between PHAST and PHASTER
| Feature | PHAST (as of Jan 2011) | PHASTER |
|---|---|---|
| Viral sequence database | ~45,000 sequences | ~187,000 sequences |
| Bacterial sequence database | ~4 million sequences | ~9 million sequences, streamlined through CD-HIT filtering |
| Computing cluster | 32 CPU cores | 112 CPU cores |
| BLAST | Legacy version 2.2.16 | BLAST+ version 2.3.0+ |
| Cluster use optimization | Rudimentary | Smart partitioning of query sequences and target bacterial DB; optimized execution parameters |
| Front-end server | Shared, single CPU | 50% faster, dedicated |
| Front-end website | Perl and CGI | Ruby on Rails |
| Genome viewer | Adobe Flash | JavaScript, AngularPlasmid and D3 |
| Queuing system | Flat file | Uses Sidekiq for threading submissions |
| Recall previous user submissions | Bookmark page | “My Searches” feature or bookmark |
| Pre-computed genome results for quick query searching | 0 | >14,000 |
| Retrieve previously annotated genome results | GenBank accession or GI number only | GenBank accession, GI number, or full sequence |
| Metagenomic data handling | NA | Supported br |
Figure 1: Identified phage for varying contig lengths
Table 3: Comparison of accuracy between the PHAST (2011) and PHASTER (2016). Evaluation was performed against manual prophage annotations in 54 bacterial genomes from Casjens, S. (2003) Molecular Microbiology, 49, 277-300. Because these manual annotations are a number of years old, predicted prophages were manually inspected, and it was determined that PHASTER finds good evidence that several of these are in fact true prophages (these are marked below in Tables 4 and 5). Once the evaluation standard was adjusted to count these prophages as true positives, adjusted sensitivity and PPV values were calculated (last two rows).
| PHAST (2011) | PHASTER (2016) | |||
|---|---|---|---|---|
| Input data | GenBank annotated genome | Sequence only | GenBank annotated genome | Sequence only |
| Sensitivity | 85.4% | 79.4% | 86.9% | 85.0% |
| Positive predictive value (PPV) | 94.2% | 86.5% | 91.0% | 87.3% |
| Prophages annotated in evaluation set | 267 | 267 | 267 | 267 |
| Prophages matched | 228 | 212 | 232 | 227 |
| Predicted prophages not present in evaluation set | 14 | 33 | 23 | 33 |
| Predicted prophages not in the evaluation set with evidence suggestive of being true prophages | N/A | N/A | 12 | 11 |
| Adjusted sensitivity | N/A | N/A | 87.5% | 85.6% |
| Adjusted PPV | N/A | N/A | 95.7% | 91.5% |
Table 4: Detailed evaluation results for PHAST (2011) and PHASTER (2016) run on GenBank annotated genomes. Evaluation was made against manual prophage annotations in 54 bacterial genomes from Casjens, S. (2003) Molecular microbiology, 49, 277-300. Prophages predicted by PHASTER that were absent in the evaluation set were manually inspected, and several (marked below with **) were deemed to have good evidence of being true prophages rather than being false positives.
==================================================================
NCBI id: NC_000962
Organism: Mycobacterium tuberculosis H37Rv
Gnome size: 4411532 bp
..................................................................
reference PHAST PHASTER
..................................................................
2970551-2981576 2970065-2983874 2970063-2983874
1780643-1788505 1766989-1788505 1766987-1788505
==================================================================
NCBI id: NC_000913
Organism: Escherichia coli K12
Gnome size: 4639675 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
262552-296320 262124-296432 262898-297206
2464567-2475651 2464378-2475651 2465301-2477629
2754181-2775804 2753821-2780748 2754896-2777782
564038-584856 563980-585282 564755-586057
1410024-1432281 1404587-1432838 1395952-1435051
1196090-1210402 1191881-1218961 1196867-1216671
1631063-1650732 1631063-1662537 1619557-1656744
2556793-2563354 FN FN
2064329-2076158 FN FN
FALSE POSITIVES 4505466-4540762 3716547-3722049
4491197-4548442 **
==================================================================
NCBI id: NC_003112
Organism: Neisseria meningitidis MC58
Gnome size: 2272360 bp
..................................................................
reference PHAST PHASTER
..................................................................
1001560-1005455 998362-1007364 FN
1099910-1133980 1101164-1133760 1101164-1133760
==================================================================
NCBI id: NC_002947
Organism: Pseudomonas putida KT2440
Gnome size: 6181863 bp
..................................................................
reference PHAST PHASTER
..................................................................
4372649-4427414 4375285-4412410 4375283-4415646
4405478-4435736
2586633-2625819 2586633-2625819 FN
3418567-3447235 3411568-3447570 3411566-3447568
1738082-1774805 1748226-1781071 1734863-1780106
==================================================================
NCBI id: NC_003902
Organism: Xanthomonas campestris pv. campestris str. ATCC 33913
Gnome size: 5076188 bp
..................................................................
reference PHAST PHASTER
..................................................................
2435595-2441676 2423307-2465702 2423305-2465700
3523234-3560198 3517532-3560198 3523035-3562020
2441850-2447920 2423307-2465702 2423305-2465700
FALSE POSITIVES 1855984-1886789 4258232-4274508
==================================================================
NCBI id: NC_002935
Organism: Corynebacterium diphtheriae NCTC 13129
Gnome size: 2488635 bp
..................................................................
reference PHAST PHASTER
..................................................................
776521-790960 FN FN
2216802-2297805 FN FN
1866723-1880855 FN 1863158-1880855
154365-190992 151932-190743 151930-190741
==================================================================
NCBI id: NC_003198
Organism: Salmonella enterica subsp. enterica serovar Typhi str. CT18
Gnome size: 4809037 bp
..................................................................
reference PHAST PHASTER
..................................................................
1888674-1933558 1879228-1939495 1879226-1937407
3515470-3548975 3511575-3552602 3504242-3555052
1538899-1572919 1538899-1572919 1538899-1572919
4473973-4507270 4462430-4507604 4462428-4507602
1008747-1052755 1008700-1053062 1008698-1053060
4683853-4694545 4683672-4695076 4683670-4695074
2760475-2768771 FN FN
==================================================================
NCBI id: NC_004337
Organism: Shigella flexneri 2a str. 301
Gnome size: 4607203 bp
..................................................................
reference PHAST PHASTER
..................................................................
2227585-2235565 FN 2229979-2240203
238841-251370 235830-252705 235830-252705
899706-918668 898668-918668 898668-918668
311291-328079 306585-340777 306583-340775
2683559-2698944 2680811-2695524 2684932-2695524
1919854-1942697 1915150-1945164 1915150-1946940
2049694-2066397 2032769-2079336 2030315-2079334
1175319-1188408 1174912-1189402 1174910-1189400
1395280-1421884 1387236-1426965 1387236-1407895
1409936-1425018
696659-747734 696659-752084 696659-752084
FALSE POSITIVES 1081687-1103027
==================================================================
NCBI id: NC_002967
Organism: Treponema denticola ATCC 35405
Gnome size: 2843201 bp
..................................................................
reference PHAST PHASTER
..................................................................
1169950-1202411 1164701-1202621 1175279-1214754
==================================================================
NCBI id: NC_002737
Organism: Streptococcus pyogenes M1 GAS
Gnome size: 1852441 bp
..................................................................
reference PHAST PHASTER
..................................................................
527569-571887 529593-570496 526682-570494
1773458-1782822 1773439-1786764 1773437-1786762
778642-820599 777508-820962 775802-821679
1192854-1222549 1182570-1222912 1182568-1222912
==================================================================
NCBI id: NC_003030
Organism: Clostridium acetobutylicum ATCC 824
Gnome size: 3940880 bp
..................................................................
reference PHAST PHASTER
..................................................................
2024020-2074254 2017739-2083829 2013351-2078513
1277643-1346789 FN 1274369-1283638
==================================================================
NCBI id: NC_003116
Organism: Neisseria meningitidis Z2491
Gnome size: 2184406 bp
..................................................................
reference PHAST PHASTER
..................................................................
1768546-1807515 1770842-1807515 1768546-1807515
1131796-1138899 1129591-1138899 1129591-1138899
1207416-1236260 1214074-1225850 FN
==================================================================
NCBI id: NC_004431
Organism: Escherichia coli CFT073
Gnome size: 5231428 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
1169792-1228729 FN FN
909332-942273 907025-945470 908948-945468
3019963-3065315 3007214-3065315 3007212-3065718
4923133-4929628 FN FN
1397370-1452231 1394721-1452257 1394721-1452255
1378215-1388952 1377875-1389094 1377873-1389092
1327053-1372820 1327916-1375035 1327914-1375035
FALSE POSITIVES 4955800-4971387 236993-283987 **
4961854-4967870 **
==================================================================
NCBI id: NC_004116
Organism: Streptococcus agalactiae 2603V/R
Gnome size: 2160267 bp
..................................................................
reference PHAST PHASTER
..................................................................
1833318-1867117 1816885-1876443 1816883-1876441
558254-599207 554829-600594 554829-601907
FALSE POSITIVES 1944858-1978401
==================================================================
NCBI id: NC_002745
Organism: Staphylococcus aureus subsp. aureus N315
Gnome size: 2814816 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
2005924-2049520 2005721-2052732 2005721-2052732
FALSE POSITIVES 2054348-2076507 2054346-2074317 **
==================================================================
NCBI id: NC_002662
Organism: Lactococcus lactis subsp. lactis Il1403
Gnome size: 2365589 bp
..................................................................
reference PHAST PHASTER
..................................................................
1036642-1071558 1033815-1079175 1033815-1079173
502723-513742 502338-520485 502338-520485
35516-49727 28461-56371 28459-56369
1414112-1456949 1414112-1457046 1414112-1457044
2013685-2025635 1997701-2028023 1997699-2028023
447236-483244 443651-484066 447143-484064
==================================================================
NCBI id: NC_002516
Organism: Pseudomonas aeruginosa PAO1
Gnome size: 6264404 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
689236-702529 673191-703058 670089-703058
672777-689221 673191-703058 670089-703058
FALSE POSITIVES 780997-796776 780995-796776 **
==================================================================
NCBI id: NC_005085
Organism: Chromobacterium violaceum ATCC 12472
Gnome size: 4751080 bp
..................................................................
reference PHAST PHASTER
..................................................................
2303969-2334742 2300705-2339162 2300705-2339162
353384-372826 353384-374417 353384-378213
428568-450397 427983-450397 427983-450397
==================================================================
NCBI id: NC_000964
Organism: Bacillus subtilis subsp. subtilis str. 168
Gnome size: 4214630 bp
..................................................................
reference PHAST PHASTER
..................................................................
2151284-2285604 2144356-2286435 2146013-2288062
2055488-2064044 2060009-2065377 2055868-2065377
2666111-2700582 2653064-2701100 2653062-2701098
1320640-1347494 1314453-1348182 1314453-1348182
FALSE POSITIVES 1899589-1919395
724913-774196
==================================================================
NCBI id: NC_005362
Organism: Lactobacillus johnsonii NCC 533
Gnome size: 1992676 bp
..................................................................
reference PHAST PHASTER
..................................................................
327894-367791 327849-370611 327847-374448
1292553-1330377 1292072-1331686 1287749-1331686
==================================================================
NCBI id: NC_003485
Organism: Streptococcus pyogenes MGAS8232
Gnome size: 1895017 bp
..................................................................
reference PHAST PHASTER
..................................................................
293882-332714 272736-351522 277254-332714
1451844-1493373 1443375-1493373 1443373-1493373
1041280-1087739 1041280-1088722 1038487-1095615
578093-618765 578055-619104 575144-619102
1206360-1241416 1200228-1241416 1200226-1241416
==================================================================
NCBI id: NC_003366
Organism: Clostridium perfringens str. 13
Gnome size: 3031430 bp
..................................................................
reference PHAST PHASTER
..................................................................
1298199-1327800 1310119-1335464 1310119-1327800
==================================================================
NCBI id: NC_003923
Organism: Staphylococcus aureus subsp. aureus MW2
Gnome size: 2820462 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
2046605-2088749 2036090-2091958 2036088-2091958
1529381-1573005 1522195-1584851 1522193-1584849
FALSE POSITIVES 836064-854951 826277-860029 **
==================================================================
NCBI id: NC_005126
Organism: Photorhabdus luminescens subsp. laumondii TTO1
Gnome size: 5688987 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
2552735-2573940 FN FN
4190163-4242791 FN FN
4340686-4389134 4340329-4385481 4324782-4373679
5175988-5190589 FN FN
2088101-2101272 FN FN
2800483-2848507 FN FN
3774756-3892173 FN FN
5201181-5228815 FN FN
4006891-4056690 4007651-4076282 4005528-4094743
1267570-1617919 FN FN
2331853-2466741 2354923-2387906 FN
2955621-2991661 FN FN
3409531-3537385 3405940-3468149 3397151-3480006
3512834-3535879 3517195-3537385
10251-29999 10251-32806 10251-32806
132320-180394 FN FN
FALSE POSITIVES 4080520-4099672 490798-502770
1785333-1795520
1983763-1993171 **
5091596-5102153
5559641-5566514 **
==================================================================
NCBI id: NC_004631
Organism: Salmonella enterica subsp. enterica serovar Typhi Ty2
Gnome size: 4791961 bp
..................................................................
reference PHAST PHASTER
..................................................................
4458029-4490856 4446023-4491190 4446021-4491188
4671630-4678034 4666561-4677964 4666559-4677962
1928058-1972330 1928058-1972330 1928058-1972330
2735202-2754628 2735079-2771942 2734604-2759926
1314607-1441766 1408218-1441766 1408218-1441766
3501128-3538076 3497233-3538262 3489900-3540712
==================================================================
NCBI id: NC_003143
Organism: Yersinia pestis CO92
Gnome size: 4653728 bp
..................................................................
reference PHAST PHASTER
..................................................................
964013-971311 FN FN
1392489-1416524 FN FN
1233128-1243405 1219764-1253174 1219762-1253172
2554373-2563203 FN 2555162-2562034
2363019-2413098 2364324-2376936 2364324-2404493
2379304-2404493
2115626-2122603 FN 2115553-2124318
==================================================================
NCBI id: NC_004668
Organism: Enterococcus faecalis V583
Gnome size: 3218031 bp
..................................................................
reference PHAST PHASTER
..................................................................
1398097-1443843 1398053-1447105 1398051-1447105
2817287-2829554 2815980-2832090 2815978-2832090
2004910-2048146 2002278-2020730 2001579-2020730
2021650-2049919 2023234-2049919
1245337-1259965 1242193-1259965 1245337-1259965
2700666-2736808 2697272-2736808 2697272-2736808
1923000-1962485 1933729-1948114 1933729-1948114
289354-326185 288968-332966 288966-332964
==================================================================
NCBI id: NC_003295
Organism: Ralstonia solanacearum GMI1000
Gnome size: 3716413 bp
..................................................................
reference PHAST PHASTER
..................................................................
2084602-2124346 2080692-2125142 2084443-2125140
1003644-1018473 FN FN
1781995-1823953 1781782-1824226 1797957-1821238
2049204-2056036 FN FN
3486521-3505550 FN 3479557-3495896
2684129-2695788 FN FN
1591303-1598986 FN FN
879632-939437 879632-899438 883334-899438
==================================================================
NCBI id: NC_003155
Organism: Streptomyces avermitilis MA-4680
Gnome size: 9025608 bp
..................................................................
reference PHAST PHASTER
..................................................................
6670511-6721444 6673473-6695725 6678303-6693625
==================================================================
NCBI id: NC_004347
Organism: Shewanella oneidensis MR-1
Gnome size: 4969803 bp
..................................................................
reference PHAST PHASTER
..................................................................
2788307-2822836 2788307-2822836 2788307-2822836
669361-703908 668166-708836 655830-720989
3075409-3126249 3069342-3114478 3069340-3114921
==================================================================
NCBI id: NC_004741
Organism: Shigella flexneri 2a str. 2457T
Gnome size: 4599354 bp
..................................................................
reference PHAST PHASTER
..................................................................
238511-254700 234959-256034 234959-256034
1177837-1191596 1177792-1192294 1177790-1192292
1614219-1620622 1612576-1617991 1612576-1617991
1619869-1623357 1619869-1623357
2021895-2044342 2013831-2041709 2003138-2057970
313843-327223 309137-339911 309135-339909
1912634-1921793 1872285-1932001 1872283-1931999
710297-746123 692891-746123 692891-743892
1901037-1921793 1872285-1932001 1872283-1931999
897790-930670 893482-915474 893482-915474
2678519-2687517 2674398-2688968 2674398-2688968
1100131-1105919 1084467-1105919 1084465-1105919
692891-709118 692891-746123 692891-743892
FALSE POSITIVES 2201408-2208976
2211660-2219625
==================================================================
NCBI id: NC_004088
Organism: Yersinia pestis KIM
Gnome size: 4600755 bp
..................................................................
reference PHAST PHASTER
..................................................................
2693615-2700576 2691227-2700576 2691227-2700576
3389410-3399754 3389138-3410723 3381641-3415033
3595228-3601343 FN FN
2417129-2456467 2415700-2456467 2415700-2456467
3237524-3255252 3237524-3247743 3237524-3247743
==================================================================
NCBI id: NC_004556
Organism: Xylella fastidiosa Temecula1
Gnome size: 2519802 bp
..................................................................
reference PHAST PHASTER
..................................................................
2005731-2020421 2005731-2022616 2005731-2022616
1847752-1855582 FN FN
1161143-1217907 1161143-1180387 1161143-1180387
1189753-1221390 1189751-1221388
1117952-1142627 1117952-1143372 1128417-1143372
454017-467611 450825-469025 450825-469025
1288547-1392763 1288547-1331541 1288023-1331541
1361920-1394823 1361918-1394821
1550281-1556188 FN FN
FALSE POSITIVES 941347-956040
==================================================================
NCBI id: NC_003997
Organism: Bacillus anthracis str. Ames
Gnome size: 5227293 bp
..................................................................
reference PHAST PHASTER
..................................................................
447387-484339 447158-484420 447156-484418
3745958-3791042 3743583-3795998 3743581-3795996
3456916-3505685 3451329-3524720 3451327-3524718
4842149-4858240 4845037-4858240 4828728-4859679
FALSE POSITIVES 1182398-1196378
==================================================================
NCBI id: NC_004578
Organism: Pseudomonas syringae pv. tomato str. DC3000
Gnome size: 6397126 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
4515380-4530373 4528892-4563495 4505488-4530373
4528890-4566113
625118-647483 FN 628136-656971
2252628-2264999 2253746-2271122 2253004-2271122
3824683-3865352 3824687-3865357 3824685-3865355
4543843-4563495 4528892-4563495 4528890-4566113
FALSE POSITIVES 4443121-4460297 **
==================================================================
NCBI id: NC_004567
Organism: Lactobacillus plantarum WCFS1
Gnome size: 3308274 bp
..................................................................
reference PHAST PHASTER
..................................................................
590128-633804 589964-633123 589608-633123
2161732-2203820 2156168-2225486 2156166-2225484
2998563-3007280 2983802-3011139 2983800-3011137
2204171-2218342 2156168-2225486 2156166-2225484
==================================================================
NCBI id: NC_002488
Organism: Xylella fastidiosa 9a5c
Gnome size: 2679306 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
489619-530138 497039-523687 506050-523687
2008224-2022372 FN 2006087-2024354
649115-690375 647732-697035 647732-697033
2361812-2404268 2351906-2408259 2348689-2388777
2177071-2183135 2176140-2198391 2157002-2184206
1514347-1541075 1514347-1540790 1514344-1557570
1585980-1631056 1585875-1640907 1585873-1640907
FALSE POSITIVES 1779582-1788942 **
2638610-2658009 **
==================================================================
NCBI id: NC_002678
Organism: Mesorhizobium loti MAFF303099
Gnome size: 7036071 bp
..................................................................
reference PHAST PHASTER
..................................................................
6975631-7011591 6975487-7020725 6975231-7011108
313639-359457 318704-347654 321147-347654
6587513-6595756 FN 6592538-6608727
==================================================================
NCBI id: NC_003210
Organism: Listeria monocytogenes EGD-e
Gnome size: 2944528 bp
..................................................................
reference PHAST PHASTER
..................................................................
2361897-2400243 2360908-2403235 2360908-2403235
120654-131380 120654-136290 120654-131380
==================================================================
NCBI id: NC_002695
Organism: Escherichia coli O157:H7 str. Sakai
Gnome size: 5498450 bp
..................................................................
reference PHAST PHASTER
..................................................................
2158314-2203914 2156899-2247627 2153413-2253837
300072-310238 300014-310600 300052-323524
1161297-1210641 1161098-1210748 1159810-1186416
1180157-1209126
5041093-5079469 5041093-5082381 5041814-5082381
1245217-1308182 1245905-1316399 1245903-1316397
1921472-1970014 1921443-1972369 1921441-1972367
2896151-2943747 2888774-2947429 2888774-2947429
3480256-3505039 3476233-3500191 3474905-3498417
310806-324405 310756-324405 300052-323524
892240-929292 892240-928363 892240-928363
1594751-1609184 1586046-1623577 1586046-1623575
1541626-1589842 1538645-1591832 1538645-1591830
1586046-1623577 1586046-1623575
3193144-3200085 3192962-3201514 3190520-3204375
2593128-2612026 2592961-2614081 2592106-2614079
2667460-2713016 2668009-2712038 2668007-2712036
1618212-1665394 1586046-1623577 1586046-1623575
1609998-1656531 1615552-1666524
1756865-1804219 1743558-1811658 1743556-1811656
2211826-2254161 2156899-2247627 2153413-2253837
FALSE POSITIVES 1437802-1446999
==================================================================
NCBI id: NC_004307
Organism: Bifidobacterium longum NCC2705
Gnome size: 2256640 bp
..................................................................
reference PHAST PHASTER
..................................................................
1298692-1312867 1288884-1312867 1288882-1312867
==================================================================
NCBI id: NC_004310
Organism: Brucella suis 1330
Gnome size: 2107794 bp
..................................................................
reference PHAST PHASTER
..................................................................
578085-584879 578578-587942 578578-588373
==================================================================
NCBI id: NC_003212
Organism: Listeria innocua Clip11262
Gnome size: 3011208 bp
..................................................................
reference PHAST PHASTER
..................................................................
78505-114250 74218-115503 74218-115501
155931-166661 151526-171570 151526-166661
2407382-2445891 2405898-2462230 2406426-2446744
1246563-1294235 1245851-1297056 1245851-1297054
2591482-2625807 2580954-2629862 2580952-2629860
1713958-1762089 1710191-1767458 1710189-1767456
==================================================================
NCBI id: NC_003197
Organism: Salmonella typhimurium LT2
Gnome size: 4857432 bp
..................................................................
reference PHAST PHASTER
..................................................................
2728976-2776816 2728976-2776892 2728976-2780003
962612-1006517 961043-1004271 961043-1006517
2042050-2059909 FN FN
2844427-2879233 2836644-2885744 2836642-2885742
2330961-2345217 2327474-2345217 FN
4417918-4438335 4417918-4438335 4417918-4438335
1098228-1143714 1098181-1144022 1098179-1144020
==================================================================
NCBI id: NC_004557
Organism: Clostridium tetani E88
Gnome size: 2799251 bp
..................................................................
reference PHAST PHASTER
..................................................................
1138054-1181003 1137516-1171268 1137516-1192459
1663821-1696302 1657698-1693073 1657696-1693071
2242455-2281387 2245647-2282092 2248862-2282092
==================================================================
NCBI id: NC_000907
Organism: Haemophilus influenzae Rd KW20
Gnome size: 1830138 bp
..................................................................
reference PHAST PHASTER
..................................................................
1559962-1594275 1558774-1597183 1558774-1597183
1499076-1513073 1495051-1513073 1495049-1513073
==================================================================
NCBI id: NC_002570
Organism: Bacillus halodurans C-125
Gnome size: 4202352 bp
..................................................................
reference PHAST PHASTER
..................................................................
10970-22161 FN FN
1381009-1384348 FN FN
1028696-1039160 1025611-1043075 1025611-1043075
3617919-3652122 3617737-3655581 3617736-3658248
FALSE POSITIVES 3783921-3800789
==================================================================
NCBI id: NC_004070
Organism: Streptococcus pyogenes MGAS315
Gnome size: 1900521 bp
..................................................................
reference PHAST PHASTER
..................................................................
1313282-1351250 1313282-1354214 1313282-1354212
749213-788176 742916-788642 742914-788640
1137743-1171867 1131000-1172231 1130998-1172231
1410725-1450458 1398708-1455522 1398706-1455520
977738-1018193 977437-1019176 974608-1026068
1230304-1271815 1227589-1283430 1227589-1283428
==================================================================
NCBI id: NC_004722
Organism: Bacillus cereus ATCC 14579
Gnome size: 5411809 bp
..................................................................
reference PHAST PHASTER
..................................................................
1805567-1866036 1803337-1866036 1803335-1866036
2531805-2565093 2520846-2580417 2520823-2579367
2355784-2369311 FN FN
3660466-3668825 3655939-3668825 3655937-3668825
FALSE POSITIVES 5089874-5096357
==================================================================
NCBI id: NC_002978
Organism: Wolbachia endosymbiont of Drosophila melanogaster
Gnome size: 1267782 bp
..................................................................
reference PHAST PHASTER
..................................................................
567453-582561 560258-580671 560258-573485
245829-275225 253155-278902 253153-278900
551654-558625 548107-556883 548107-556883
623343-634537 622819-636172 614233-650482
==================================================================
NCBI id: NC_002655
Organism: Escherichia coli O157:H7 EDL933
Gnome size: 5528445 bp
..................................................................
reference PHAST PHASTER
..................................................................
1879335-1897622 1835962-1931572 1835960-1935058
3551577-3565707 3546082-3567481 3544754-3565707
2966382-3015014 2959005-3018696 2959005-3018696
2668339-2688870 2668172-2689292 2667317-2692188
2285976-2330172 2272363-2331832 2272753-2342415
300073-310251 300055-324556 300053-323525
1897625-1908911 1835962-1931572 1835960-1935058
1702185-1725748 1693971-1748316 1670022-1705963
1693969-1748314
310756-323112 300055-324556 300053-323525
1250521-1295458 1250321-1295565 1249033-1295563
1330857-1391923 1330722-1400171 1330720-1400169
1678706-1693737 1678682-1693909 1670022-1705963
1849488-1879269 1835962-1931572 1835960-1935058
1909139-1930250 1835962-1931572 1835960-1935058
892845-930943 892759-931347 892757-931345
1730065-1756006 1693971-1748316 1693969-1748314
1748352-1756006
1626722-1673485 1623741-1675808 1623741-1675806
1670022-1705963
2743223-2788348 2743226-2797853 2743224-2788401
2118738-2165694 2107529-2165694 2116354-2148177
2142480-2177204
3263064-3270404 3262918-3271470 3260476-3274334
==================================================================
NCBI id: NC_004606
Organism: Streptococcus pyogenes SSI-1
Gnome size: 1894275 bp
..................................................................
reference PHAST PHASTER
..................................................................
1107957-1147543 1098748-1161350 1098746-1161348
725017-759141 724653-759313 724653-759311
446427-486160 441338-498168 441336-498166
625070-666334 624977-669296 623853-669296
545636-583603 545489-583680 545487-583678
878690-919064 877707-924830 877707-924828
==================================================================
NCBI id: NC_002758
Organism: Staphylococcus aureus subsp. aureus Mu50
Gnome size: 2878529 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
917507-962565 917452-961932 910703-961979
2083515-2126110 2082982-2129322 2069951-2129411
2124924-2152937 2124922-2150747
FALSE POSITIVES 1936945-1959426 854223-895164 **
865041-882822
==================================================================
NCBI id: NC_003919
Organism: Xanthomonas axonopodis pv. citri str. 306
Gnome size: 5175554 bp
..................................................................
reference PHAST PHASTER
..................................................................
3105263-3115868 3081511-3128919 3081509-3127792
1211424-1228677 1220880-1228677 1209301-1229038
==================================================================
Table 5: Detailed evaluation results for PHAST (2011) and PHASTER (2016) run on unannotated genome sequences. Evaluation was made against manual prophage annotations in 54 bacterial genomes from Casjens, S. (2003) Molecular microbiology, 49, 277-300. Prophages predicted by PHASTER that were absent in the evaluation set were manually inspected, and several (marked below with **) were deemed to have good evidence of being true prophages rather than being false positives.
==================================================================
NCBI id: NC_000962
Organism: Mycobacterium tuberculosis H37Rv
Gnome size: 4411532 bp
..................................................................
reference PHAST PHASTER
..................................................................
2970551-2981576 2970065-2980835 2970063-2980833
1780643-1788505 FN 1766987-1788115
==================================================================
NCBI id: NC_000913
Organism: Escherichia coli K12
Gnome size: 4639675 bp
..................................................................
reference PHAST PHASTER
..................................................................
262552-296320 FN FN
2464567-2475651 FN 2465301-2477629
2754181-2775804 FN FN
564038-584856 563980-585282 564755-586057
1410024-1432281 1409925-1432985 1411899-1434959
1196090-1210402 1197865-1215896 1198640-1216671
1631063-1650732 1616881-1650732 1627517-1644304
2556793-2563354 FN FN
2064329-2076158 FN FN
FALSE POSITIVES 3716547-3722049
==================================================================
NCBI id: NC_003112
Organism: Neisseria meningitidis MC58
Gnome size: 2272360 bp
..................................................................
reference PHAST PHASTER
..................................................................
1001560-1005455 998266-1007364 FN
1099910-1133980 1099110-1133760 1101164-1133966
FALSE POSITIVES 916111-930967 916109-929811
==================================================================
NCBI id: NC_002947
Organism: Pseudomonas putida KT2440
Gnome size: 6181863 bp
..................................................................
reference PHAST PHASTER
..................................................................
4372649-4427414 4375285-4412410 4375283-4412410
4417270-4440874
2586633-2625819 2585881-2626121 2586645-2608847
3418567-3447235 3401670-3459949 3426049-3447235
1738082-1774805 1734865-1780108 1748035-1781069
==================================================================
NCBI id: NC_003902
Organism: Xanthomonas campestris pv. campestris str. ATCC 33913
Gnome size: 5076188 bp
..................................................................
reference PHAST PHASTER
..................................................................
2435595-2441676 FN 2435792-2454339
3523234-3560198 3517532-3560198 3523035-3562020
2441850-2447920 FN 2435792-2454339
FALSE POSITIVES 1855984-1886789 4258232-4274508
==================================================================
NCBI id: NC_002935
Organism: Corynebacterium diphtheriae NCTC 13129
Gnome size: 2488635 bp
..................................................................
reference PHAST PHASTER
..................................................................
776521-790960 FN FN
2216802-2297805 FN FN
1866723-1880855 FN 1863158-1880771
154365-190992 151932-190743 151930-190741
==================================================================
NCBI id: NC_003198
Organism: Salmonella enterica subsp. enterica serovar Typhi str. CT18
Gnome size: 4809037 bp
..................................................................
reference PHAST PHASTER
..................................................................
1888674-1933558 1885617-1927047 1885326-1933598
3515470-3548975 3511575-3552602 3504242-3555052
1538899-1572919 1538899-1572919 1538899-1572919
4473973-4507270 4459146-4507270 4459144-4507514
1008747-1052755 1008700-1053062 1008698-1053060
4683853-4694545 4683672-4696075 4683670-4696075
2760475-2768771 FN FN
FALSE POSITIVES 1781177-1787337 1079782-1090874
1781177-1789457
==================================================================
NCBI id: NC_004337
Organism: Shigella flexneri 2a str. 301
Gnome size: 4607203 bp
..................................................................
reference PHAST PHASTER
..................................................................
2227585-2235565 2220680-2241353 2220680-2240203
238841-251370 236055-252705 236055-252705
899706-918668 899339-921295 899339-921295
311291-328079 306585-340777 306583-340775
2683559-2698944 FN 2684932-2695524
1919854-1942697 1916802-1945128 1916802-1946940
2049694-2066397 2032769-2079336 2030315-2079334
1175319-1188408 1174944-1188408 1174944-1188408
1395280-1421884 1373649-1427197 1387236-1407895
1401123-1425759
696659-747734 696659-749966 696659-747734
FALSE POSITIVES 2352233-2367765 492546-495944
2950035-2958559 1081687-1103027
3051242-3094081 1574398-1580656
1574398-1583708 3687621-3693861
==================================================================
NCBI id: NC_002967
Organism: Treponema denticola ATCC 35405
Gnome size: 2843201 bp
..................................................................
reference PHAST PHASTER
..................................................................
1169950-1202411 1164701-1202621 1175279-1214754
==================================================================
NCBI id: NC_002737
Organism: Streptococcus pyogenes M1 GAS
Gnome size: 1852441 bp
..................................................................
reference PHAST PHASTER
..................................................................
527569-571887 529593-570496 526682-570494
1773458-1782822 FN FN
778642-820599 777508-820962 775802-821679
1192854-1222549 1182570-1222912 1182568-1222912
==================================================================
NCBI id: NC_003030
Organism: Clostridium acetobutylicum ATCC 824
Gnome size: 3940880 bp
..................................................................
reference PHAST PHASTER
..................................................................
2024020-2074254 2017739-2083829 2013351-2078513
1277643-1346789 FN 1274369-1283638
==================================================================
NCBI id: NC_003116
Organism: Neisseria meningitidis Z2491
Gnome size: 2184406 bp
..................................................................
reference PHAST PHASTER
..................................................................
1768546-1807515 1770842-1807515 1768546-1807515
1131796-1138899 FN FN
1207416-1236260 1211167-1236054 1218293-1236260
==================================================================
NCBI id: NC_004431
Organism: Escherichia coli CFT073
Gnome size: 5231428 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
1169792-1228729 FN FN
909332-942273 907025-945470 908948-945468
3019963-3065315 3007214-3065315 3007212-3065315
4923133-4929628 FN FN
1397370-1452231 1394721-1452257 1394721-1452255
1378215-1388952 1327942-1397351 1324666-1381279
1327053-1372820 1327942-1397351 1324666-1381279
FALSE POSITIVES 244220-257682 244220-265366 **
==================================================================
NCBI id: NC_004116
Organism: Streptococcus agalactiae 2603V/R
Gnome size: 2160267 bp
..................................................................
reference PHAST PHASTER
..................................................................
1833318-1867117 1816885-1876443 1816883-1876441
558254-599207 550500-617296 550498-617294
FALSE POSITIVES 1944854-1978401
==================================================================
NCBI id: NC_002745
Organism: Staphylococcus aureus subsp. aureus N315
Gnome size: 2814816 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
2005924-2049520 2005721-2052732 2005721-2052732
FALSE POSITIVES 2054348-2076507 2054346-2074317 **
1859152-1881615
==================================================================
NCBI id: NC_002662
Organism: Lactococcus lactis subsp. lactis Il1403
Gnome size: 2365589 bp
..................................................................
reference PHAST PHASTER
..................................................................
1036642-1071558 1033815-1077533 1033815-1077531
502723-513742 502338-520485 502338-517610
35516-49727 28461-56371 28459-56369
1414112-1456949 1414112-1457046 1414112-1457044
2013685-2025635 1997701-2028023 1997699-2028023
447236-483244 443687-484066 447143-484064
==================================================================
NCBI id: NC_002516
Organism: Pseudomonas aeruginosa PAO1
Gnome size: 6264404 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
689236-702529 673191-701381 670089-701381
672777-689221 673191-701381 670089-701381
FALSE POSITIVES 780997-796776 780995-796776 **
==================================================================
NCBI id: NC_005085
Organism: Chromobacterium violaceum ATCC 12472
Gnome size: 4751080 bp
..................................................................
reference PHAST PHASTER
..................................................................
2303969-2334742 2300705-2344086 2300705-2339162
353384-372826 353384-374612 353384-378213
428568-450397 427983-449939 427983-447996
==================================================================
NCBI id: NC_000964
Organism: Bacillus subtilis subsp. subtilis str. 168
Gnome size: 4214630 bp
..................................................................
reference PHAST PHASTER
..................................................................
2151284-2285604 2151626-2290857 2151626-2288090
2055488-2064044 FN FN
2666111-2700582 2653064-2701100 2653062-2701098
1320640-1347494 1325096-1348182 1314453-1348182
==================================================================
NCBI id: NC_005362
Organism: Lactobacillus johnsonii NCC 533
Gnome size: 1992676 bp
..................................................................
reference PHAST PHASTER
..................................................................
327894-367791 327849-370611 327847-374448
1292553-1330377 1292072-1331686 1287749-1331686
==================================================================
NCBI id: NC_003485
Organism: Streptococcus pyogenes MGAS8232
Gnome size: 1895017 bp
..................................................................
reference PHAST PHASTER
..................................................................
293882-332714 283161-348115 277254-332714
1451844-1493373 1443375-1493373 1443373-1493373
1041280-1087739 1041280-1088722 1038487-1095615
578093-618765 578055-619104 575144-619102
1206360-1241416 1200228-1241780 1200226-1241780
==================================================================
NCBI id: NC_003366
Organism: Clostridium perfringens str. 13
Gnome size: 3031430 bp
..................................................................
reference PHAST PHASTER
..................................................................
1298199-1327800 1310119-1335464 1310119-1327800
==================================================================
NCBI id: NC_003923
Organism: Staphylococcus aureus subsp. aureus MW2
Gnome size: 2820462 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
2046605-2088749 2036090-2091958 2036088-2091958
1529381-1573005 1522195-1584851 1522193-1584849
FALSE POSITIVES 836064-854951 836064-853794 **
==================================================================
NCBI id: NC_005126
Organism: Photorhabdus luminescens subsp. laumondii TTO1
Gnome size: 5688987 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
2552735-2573940 FN FN
4190163-4242791 FN FN
4340686-4389134 4340329-4385481 4324782-4373679
5175988-5190589 FN FN
2088101-2101272 FN FN
2800483-2848507 FN FN
3774756-3892173 FN FN
5201181-5228815 FN 5211071-5239791
4006891-4056690 4007651-4076282 4005528-4094743
1267570-1617919 FN FN
2331853-2466741 2354852-2390454 2372413-2387799
2955621-2991661 FN FN
3409531-3537385 3405940-3468149 3397086-3479941
3512834-3535879 3517195-3537385
10251-29999 10251-32806 10251-32806
132320-180394 FN FN
FALSE POSITIVES 490798-502770
1785333-1795520
1983763-1993171 **
2035298-2041677 **
5559641-5566514 **
==================================================================
NCBI id: NC_004631
Organism: Salmonella enterica subsp. enterica serovar Typhi Ty2
Gnome size: 4791961 bp
..................................................................
reference PHAST PHASTER
..................................................................
4458029-4490856 4446023-4491190 4446021-4491188
4671630-4678034 4666561-4678557 4666559-4678557
1928058-1972330 1928058-1972330 1927739-1972365
2735202-2754628 2734606-2760158 2734604-2760158
1314607-1441766 1408218-1441766 1408218-1441766
3501128-3538076 3497233-3538262 3489900-3540712
FALSE POSITIVES 1193795-1199955 1193795-1199955
==================================================================
NCBI id: NC_003143
Organism: Yersinia pestis CO92
Gnome size: 4653728 bp
..................................................................
reference PHAST PHASTER
..................................................................
964013-971311 FN 954442-989832
1392489-1416524 FN FN
1233128-1243405 FN FN
2554373-2563203 FN FN
2363019-2413098 2362962-2404686 2362960-2404684
2115626-2122603 FN 2111358-2140547
FALSE POSITIVES 1807069-1816414
==================================================================
NCBI id: NC_004668
Organism: Enterococcus faecalis V583
Gnome size: 3218031 bp
..................................................................
reference PHAST PHASTER
..................................................................
1398097-1443843 1398053-1447105 1398051-1446151
2817287-2829554 FN FN
2004910-2048146 2021650-2049919 2001579-2020730
2023234-2049919
1245337-1259965 1242193-1259965 1245337-1259965
2700666-2736808 2697272-2736808 2697272-2736808
1923000-1962485 1925423-1948114 1925423-1948114
289354-326185 288968-332966 288966-332964
FALSE POSITIVES 2537668-2551243
551891-566251
==================================================================
NCBI id: NC_003295
Organism: Ralstonia solanacearum GMI1000
Gnome size: 3716413 bp
..................................................................
reference PHAST PHASTER
..................................................................
2084602-2124346 2080692-2125142 2084443-2125140
1003644-1018473 FN FN
1781995-1823953 1782598-1838886 1798179-1821238
2049204-2056036 FN FN
3486521-3505550 FN FN
2684129-2695788 FN FN
1591303-1598986 FN FN
879632-939437 879632-899438 887600-899438
FALSE POSITIVES 3456925-3462472
==================================================================
NCBI id: NC_003155
Organism: Streptomyces avermitilis MA-4680
Gnome size: 9025608 bp
..................................................................
reference PHAST PHASTER
..................................................................
6670511-6721444 6673473-6693625 6678303-6693625
==================================================================
NCBI id: NC_004347
Organism: Shewanella oneidensis MR-1
Gnome size: 4969803 bp
..................................................................
reference PHAST PHASTER
..................................................................
2788307-2822836 2788307-2822836 2788307-2822836
669361-703908 668166-708836 655830-720989
3075409-3126249 3076443-3126351 3076443-3126349
FALSE POSITIVES 4434306-4457138
==================================================================
NCBI id: NC_004741
Organism: Shigella flexneri 2a str. 2457T
Gnome size: 4599354 bp
..................................................................
reference PHAST PHASTER
..................................................................
238511-254700 235184-256034 235184-256034
1177837-1191596 1177792-1192294 1177790-1192292
1614219-1620622 1612770-1624438 1612770-1627925
2021895-2044342 2012871-2061855 2006995-2054672
313843-327223 309137-339911 309135-339909
1912634-1921793 1872285-1932001 1893682-1923605
710297-746123 692891-748184 692891-748184
1901037-1921793 1872285-1932001 1881581-1903815
1893682-1923605
897790-930670 893482-918345 893482-918345
915755-943797 915753-943795
2678519-2687517 2674260-2688968 2678519-2688968
1100131-1105919 FN 1084465-1105919
692891-709118 692891-748184 692891-748184
FALSE POSITIVES 2047401-2074125 492349-495747
2201408-2220775 2058418-2071061
2331690-2347222 2201408-2219625
2594187-2620410
4081357-4087597
==================================================================
NCBI id: NC_004088
Organism: Yersinia pestis KIM
Gnome size: 4600755 bp
..................................................................
reference PHAST PHASTER
..................................................................
2693615-2700576 2676241-2705460 2676239-2705458
3389410-3399754 FN FN
3595228-3601343 FN 3584471-3619864
2417129-2456467 2415700-2456467 2415700-2456467
3237524-3255252 FN FN
==================================================================
NCBI id: NC_004556
Organism: Xylella fastidiosa Temecula1
Gnome size: 2519802 bp
..................................................................
reference PHAST PHASTER
..................................................................
2005731-2020421 2004606-2022616 2005890-2022616
1847752-1855582 FN FN
1161143-1217907 1161143-1180387 1161143-1180387
1170407-1224505 1194458-1217907
1117952-1142627 1128432-1143339 1132387-1143339
454017-467611 450846-469025 446956-480065
1288547-1392763 1288547-1331541 1288023-1331541
1362504-1398130 1362502-1398128
1550281-1556188 FN FN
FALSE POSITIVES 942607-968324
==================================================================
NCBI id: NC_003997
Organism: Bacillus anthracis str. Ames
Gnome size: 5227293 bp
..................................................................
reference PHAST PHASTER
..................................................................
447387-484339 442051-487498 442049-487496
3745958-3791042 3743583-3795491 3743581-3795489
3456916-3505685 3452696-3517428 3452694-3517426
4842149-4858240 4845037-4858240 4845035-4859679
==================================================================
NCBI id: NC_004578
Organism: Pseudomonas syringae pv. tomato str. DC3000
Gnome size: 6397126 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
4515380-4530373 4505490-4530373 4505488-4530373
625118-647483 FN 623546-651202
2252628-2264999 FN 2253004-2271122
3824683-3865352 3825217-3859789 3825215-3859787
4543843-4563495 4531874-4564742 4531872-4566113
FALSE POSITIVES 4442166-4460297 4442166-4460297 **
==================================================================
NCBI id: NC_004567
Organism: Lactobacillus plantarum WCFS1
Gnome size: 3308274 bp
..................................................................
reference PHAST PHASTER
..................................................................
590128-633804 589964-631772 589608-631770
2161732-2203820 2156168-2225486 2157270-2197761
2188411-2232769
2998563-3007280 FN FN
2204171-2218342 2156168-2225486 2188411-2232769
==================================================================
NCBI id: NC_002488
Organism: Xylella fastidiosa 9a5c
Gnome size: 2679306 bp
..................................................................
reference PHAST PHASTER
..................................................................
489619-530138 486958-528483 486956-528481
2008224-2022372 2005406-2022394 2006087-2024354
649115-690375 647699-697035 647699-697033
2361812-2404268 2358989-2416179 2361812-2388777
2177071-2183135 2176140-2198391 2170954-2199787
1514347-1541075 1500396-1549341 1514344-1557570
1585980-1631056 1585875-1640907 1585873-1640907
==================================================================
NCBI id: NC_002678
Organism: Mesorhizobium loti MAFF303099
Gnome size: 7036071 bp
..................................................................
reference PHAST PHASTER
..................................................................
6975631-7011591 6975487-7020725 6975231-7011108
313639-359457 313234-360978 321147-347654
6587513-6595756 FN 6592538-6608727
FALSE POSITIVES 4868226-4896693 4803034-4831740
4868224-4896691
==================================================================
NCBI id: NC_003210
Organism: Listeria monocytogenes EGD-e
Gnome size: 2944528 bp
..................................................................
reference PHAST PHASTER
..................................................................
2361897-2400243 2360908-2403235 2360908-2403235
120654-131380 120654-136290 120654-131380
FALSE POSITIVES 166687-174556
==================================================================
NCBI id: NC_002695
Organism: Escherichia coli O157:H7 str. Sakai
Gnome size: 5498450 bp
..................................................................
reference PHAST PHASTER
..................................................................
2158314-2203914 2156899-2247603 2153413-2254887
300072-310238 300054-324555 291210-317713
1161297-1210641 1161098-1210748 1159810-1178581
1180157-1209126
5041093-5079469 5041093-5082381 5042064-5079469
1245217-1308182 1245905-1316399 1245903-1316397
1921472-1970014 1921443-1972369 1921441-1972367
2896151-2943747 2888774-2947429 2888774-2947429
3480256-3505039 3479659-3500191 3479657-3500189
310806-324405 300054-324555 291210-317713
892240-929292 891110-929696 891108-929694
1594751-1609184 1586046-1621990 1586046-1621988
1541626-1589842 1541512-1591832 1538645-1591830
1586046-1621990 1586046-1621988
3193144-3200085 3192962-3201514 3191900-3201512
2593128-2612026 2592961-2614081 2592106-2616977
2667460-2713016 2668009-2712038 2668007-2712036
1618212-1665394 1586046-1621990 1586046-1621988
1609998-1656531 1615552-1666524
1756865-1804219 1770296-1823989 1757549-1814804
2211826-2254161 2156899-2247603 2153413-2254887
FALSE POSITIVES 1437802-1446999
==================================================================
NCBI id: NC_004307
Organism: Bifidobacterium longum NCC2705
Gnome size: 2256640 bp
..................................................................
reference PHAST PHASTER
..................................................................
1298692-1312867 1288884-1312690 1288882-1312690
==================================================================
NCBI id: NC_004310
Organism: Brucella suis 1330
Gnome size: 2107794 bp
..................................................................
reference PHAST PHASTER
..................................................................
578085-584879 578497-592232 578497-592232
==================================================================
NCBI id: NC_003212
Organism: Listeria innocua Clip11262
Gnome size: 3011208 bp
..................................................................
reference PHAST PHASTER
..................................................................
78505-114250 74218-115503 74218-115501
155931-166661 151526-171570 151526-166661
2407382-2445891 2405898-2462230 2406426-2446744
1246563-1294235 1245851-1297056 1245851-1297054
2591482-2625807 2580954-2629862 2580952-2629860
1713958-1762089 1710191-1767458 1710189-1767456
==================================================================
NCBI id: NC_003197
Organism: Salmonella typhimurium LT2
Gnome size: 4857432 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
2728976-2776816 2729000-2776892 2731822-2776890
962612-1006517 961043-1003236 961043-1006517
2042050-2059909 FN FN
2844427-2879233 2844267-2879414 2844265-2879414
2330961-2345217 2327474-2344711 2330961-2345217
4417918-4438335 4417918-4438335 4417918-4438335
1098228-1143714 1098181-1144022 1098179-1144020
FALSE POSITIVES 1957835-1973856 1957835-1971770 **
==================================================================
NCBI id: NC_004557
Organism: Clostridium tetani E88
Gnome size: 2799251 bp
..................................................................
reference PHAST PHASTER
..................................................................
1138054-1181003 1137606-1171268 1137606-1185305
1663821-1696302 1651670-1710164 1657696-1693071
2242455-2281387 2243717-2282092 2232193-2282092
==================================================================
NCBI id: NC_000907
Organism: Haemophilus influenzae Rd KW20
Gnome size: 1830138 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
1559962-1594275 1558774-1597183 1558774-1597183
1499076-1513073 1495051-1513250 1495049-1513250
FALSE POSITIVES 1636791-1643216 1636791-1643216 **
==================================================================
NCBI id: NC_002570
Organism: Bacillus halodurans C-125
Gnome size: 4202352 bp
..................................................................
reference PHAST PHASTER
..................................................................
10970-22161 FN FN
1381009-1384348 FN FN
1028696-1039160 1025611-1043075 1025611-1043075
3617919-3652122 3625321-3655581 3606875-3658248
FALSE POSITIVES 3783921-3800789
==================================================================
NCBI id: NC_004070
Organism: Streptococcus pyogenes MGAS315
Gnome size: 1900521 bp
..................................................................
reference PHAST PHASTER
..................................................................
1313282-1351250 1313282-1354214 1313282-1354212
749213-788176 742916-788642 742914-788640
1137743-1171867 1131000-1172231 1130998-1172231
1410725-1450458 1410544-1452968 1410542-1452968
977738-1018193 977437-1019176 974608-1026068
1230304-1271815 1227589-1283430 1227589-1283428
==================================================================
NCBI id: NC_004722
Organism: Bacillus cereus ATCC 14579
Gnome size: 5411809 bp
..................................................................
reference PHAST PHASTER
..................................................................
1805567-1866036 1803337-1866036 1803335-1866036
2531805-2565093 2520846-2580417 2520823-2579367
2355784-2369311 FN FN
3660466-3668825 3657003-3668825 3655937-3668825
FALSE POSITIVES 5089874-5096462
==================================================================
NCBI id: NC_002978
Organism: Wolbachia endosymbiont of Drosophila melanogaster
Gnome size: 1267782 bp
..................................................................
reference PHAST PHASTER
..................................................................
567453-582561 548107-572145 548107-573485
572259-584372
245829-275225 236216-278994 236214-278992
551654-558625 548107-572145 548107-573485
623343-634537 626322-642427 626320-642425
FALSE POSITIVES 437078-443628
==================================================================
NCBI id: NC_002655
Organism: Escherichia coli O157:H7 EDL933
Gnome size: 5528445 bp
..................................................................
reference PHAST PHASTER
..................................................................
1879335-1897622 1862359-1931572 1862359-1935058
3551577-3565707 3549508-3567481 3549506-3567479
2966382-3015014 2961049-3018696 2961049-3018696
2668339-2688870 2668172-2689292 2667317-2692188
2285976-2330172 2272363-2331832 2272753-2330172
300073-310251 300055-324556 291211-317714
1897625-1908911 1862359-1931572 1862359-1935058
1702185-1725748 1693971-1748316 1699525-1757930
310756-323112 300055-324556 291211-317714
1250521-1295458 1250321-1295565 1249033-1295563
1330857-1391923 1330722-1400171 1330720-1400169
1678706-1693737 1678682-1693909 1683407-1692862
1849488-1879269 1862359-1931572 1862359-1935058
1909139-1930250 1862359-1931572 1862359-1935058
892845-930943 892759-931347 892757-931345
1730065-1756006 1693971-1748316 1699525-1757930
1626722-1673485 1626608-1675808 1623741-1675806
2743223-2788348 2743226-2788403 2743224-2788401
2118738-2165694 2107529-2165694 2107527-2165694
3263064-3270404 3262918-3271470 3261856-3271468
FALSE POSITIVES 1125968-1135165
1521574-1530771
==================================================================
NCBI id: NC_004606
Organism: Streptococcus pyogenes SSI-1
Gnome size: 1894275 bp
..................................................................
reference PHAST PHASTER
..................................................................
1107957-1147543 1098748-1161350 1098746-1161348
725017-759141 724653-759313 724653-759311
446427-486160 443902-486333 443902-486331
625070-666334 624977-669296 623853-669296
545636-583603 545489-583680 545487-583678
878690-919064 877707-924830 877707-924828
==================================================================
NCBI id: NC_002758
Organism: Staphylococcus aureus subsp. aureus Mu50
Gnome size: 2878529 bp
..................................................................
reference PHAST PHASTER (** = likely true positive)
..................................................................
917507-962565 917452-961932 910703-961979
2083515-2126110 2084317-2129322 2082980-2129322
2124924-2152937 2124922-2150747
FALSE POSITIVES 1936945-1959408 854223-895164 **
865041-882822
==================================================================
NCBI id: NC_003919
Organism: Xanthomonas axonopodis pv. citri str. 306
Gnome size: 5175554 bp
..................................................................
reference PHAST PHASTER
..................................................................
3105263-3115868 3081511-3127794 3081509-3127792
1211424-1228677 FN 1209301-1229038
==================================================================