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Prophinder: supplementary materials
Evaluation procedure

The most reliable reference set to evaluate prophages prediction comes from a collection of annotated prophages provided by S. Casjens (extension from (Casjens, 2003)). The original, manually annotated, set contains 329 prophages. Prophages with less than 7 proteins were filtered out from the set since considered as too short or ambiguous.
We included in this evaluation another prophage detection method called Phage_Finder (Fouts, 2006). In order to compare prediction results between Prophinder and Phage_Finder, we took the list of screened genomes available on the Phage_Finder web site (http://phage-finder.sourceforge.net/302_bact_gen.pdf) and removed those not annotated by S. Cajens. The resulting reference set is composed of 54 genomes with 287 annotated prophages that were used for this evaluation. We want to stress out that the predictions extracted from the Phage_Finder web site were produced using conservative parameters and therefore the evaluation result presented here is not representative of the real predictive capabilities of the method. Running Phage_Finder on all bacterial genomes using optimal/optimized parameters goes beyong the scope of our work and would require too much CPU time for our compuational infrastructure. Therefore, the evaluation result for Phage_Finder is only indicative and should be interpreted with objectivity.

Out of the 54 GenBank entries used for the evaluation, 179 prophages were predicted by Phage_Finder and 238 by Prophinder.
Predicted prophages were compared to the reference set using the compare-classes program (http://rsat.scmbb.ulb.ac.be/rsat/compare-classes_form.cgi), from the RSA-Tools software package (van Helden, 2003), which assesses the statistical significance of common members between reference and predicted prophages. The raw outputs are available for Phage_Finder and Prophinder. The table below presents, for each evaluated bacterial genome, the list of prophages detected by Prophinder ('prophinder:' IDs) and Phage_Finder ('phage_finder:' IDs) with the compare-classes Evalue and the number of coding sequences in common with the reference prophages ('sherw:' IDs). False positives and false negatives for both methods are listed at the end of each GenBank table.
Two standard measures have been used to evaluate the predictive capabilities of the methods:
1) The sensitivity which is calculated as the fraction of annotated prophages that are predicted:

Sn = reference prophages detected / total reference prophages

2) The positive predictive value is the fraction of predicted prophages that are matching annotated prophages (True Positives) over the total number of predicted prophages (True Positives + False Positives):
PPV = TP / (TP + FP)

Note: since several predicted prophages can cover one reference prophage, the number of TPs can be higher than the number of reference prophages detected.

Phage_Finder gives a Sn = 0.67 and a PPV = 0.94
Prophinder gives a Sn = 0.78 and a PPV = 0.95

References
Casjens, S. (2003) Prophages and bacterial genomics: what have we learned so far?, Mol Microbiol, 49, 277-300.
Fouts, D.E. (2006) Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences, Nucleic Acids Res, 34, 5839-5851.
van Helden, J. (2003) Regulatory sequence analysis tools, Nucleic Acids Res, 31, 3593-3596.

Evaluation details
Prophages with less than 7CDS were discarded.
Number of GenBank entries: 54
Number of reference prophages: 267
Number of prophages by Prophinder: 238
Number of prophages by Phage_finder: 179

NC_000962 Mycobacterium tuberculosis H37Rv - 4411532bp  Go to Prophinder
sherw:2942970551 - 298157616CDS
phage_finder:164732969989 - 298099815CDS14 overlapping CDS - Eval: 6e-39
 
sherw:2951780643 - 178850511CDS
phage_finder:164721771924 - 178852321CDS11 overlapping CDS - Eval: 9.2e-28
 
Prophinder false negatives
sherw:2942970551 - 298157616CDS
sherw:2951780643 - 178850511CDS
 
NC_000913 Escherichia coli K12 - 4639675bp  Go to Prophinder
sherw:2801410024 - 143228125CDS
prophinder:332801410024 - 143169824CDS24 overlapping CDS - Eval: 4.1e-68
phage_finder:163981409923 - 143302525CDS25 overlapping CDS - Eval: 8.2e-73
 
sherw:2841631063 - 165073231CDS
prophinder:332831631646 - 164365719CDS19 overlapping CDS - Eval: 8.8e-48
phage_finder:163991631485 - 166254641CDS30 overlapping CDS - Eval: 5.6e-75
 
sherw:2821196090 - 121040219CDS
prophinder:332771198902 - 121040216CDS16 overlapping CDS - Eval: 1.6e-44
 
sherw:283564038 - 58485626CDS
prophinder:33276572144 - 58060215CDS15 overlapping CDS - Eval: 8.8e-38
phage_finder:16397563978 - 58532626CDS26 overlapping CDS - Eval: 1.8e-75
 
sherw:2762464567 - 247565113CDS
prophinder:332792464567 - 247453212CDS12 overlapping CDS - Eval: 8.1e-35
phage_finder:164002464376 - 247431211CDS11 overlapping CDS - Eval: 2e-31
 
Prophinder false negatives
sherw:2782754181 - 277580424CDS
sherw:281262552 - 29632038CDS
sherw:2792556793 - 25633549CDS
sherw:2772064329 - 207615812CDS
 
Phage_Finder false negatives
sherw:2782754181 - 277580424CDS
sherw:281262552 - 29632038CDS
sherw:2792556793 - 25633549CDS
sherw:2772064329 - 207615812CDS
sherw:2821196090 - 121040222CDS
 
NC_002947 Pseudomonas putida KT2440 - 6181863bp  Go to Prophinder
sherw:3022586633 - 262581932CDS
prophinder:329162586633 - 262581932CDS32 overlapping CDS - Eval: 2.4e-90
phage_finder:165072586037 - 262608232CDS32 overlapping CDS - Eval: 4e-91
 
sherw:3044372649 - 442741472CDS
prophinder:329174383855 - 440784131CDS31 overlapping CDS - Eval: 1.9e-67
phage_finder:165094371581 - 442756372CDS72 overlapping CDS - Eval: 7.7e-186
 
sherw:3051738082 - 177480550CDS
prophinder:329151753027 - 177689430CDS27 overlapping CDS - Eval: 8.5e-60
prophinder:329291738082 - 175259322CDS22 overlapping CDS - Eval: 3.4e-50
phage_finder:165061737983 - 177743153CDS50 overlapping CDS - Eval: 4.3e-131
 
sherw:3033418567 - 344723535CDS
prophinder:329183412988 - 345344344CDS35 overlapping CDS - Eval: 4.6e-89
phage_finder:165083412988 - 344723541CDS35 overlapping CDS - Eval: 4.1e-92
 
NC_003112 Neisseria meningitidis MC58 - 2272360bp  Go to Prophinder
sherw:2161099910 - 113398038CDS
prophinder:337801109535 - 113116220CDS20 overlapping CDS - Eval: 3.7e-48
phage_finder:164761099901 - 113347636CDS36 overlapping CDS - Eval: 1.9e-98
 
Prophinder false negatives
sherw:2171001560 - 10054557CDS
 
Phage_Finder false negatives
sherw:2171001560 - 10054557CDS
 
NC_002935 Corynebacterium diphtheriae NCTC 13129 - 2488635bp  Go to Prophinder
sherw:2931866723 - 188085521CDS
phage_finder:163681866360 - 188102321CDS21 overlapping CDS - Eval: 5.5e-62
 
sherw:290154365 - 19099245CDS
prophinder:33784166018 - 18749819CDS19 overlapping CDS - Eval: 1.5e-43
phage_finder:16367160942 - 18749830CDS30 overlapping CDS - Eval: 2e-74
 
Prophinder false negatives
sherw:2931866723 - 188085521CDS
sherw:291776521 - 79096020CDS
sherw:2922216802 - 229780549CDS
 
Phage_Finder false negatives
sherw:291776521 - 79096020CDS
sherw:2922216802 - 229780549CDS
 
NC_003902 Xanthomonas campestris pv. campestris str. ATCC 33913 - 5076188bp  Go to Prophinder
sherw:2373523234 - 356019851CDS
phage_finder:166803523026 - 356038851CDS51 overlapping CDS - Eval: 7.9e-138
 
Prophinder false negatives
sherw:2392441850 - 244792010CDS
sherw:2382435595 - 244167610CDS
sherw:2373523234 - 356019851CDS
 
Phage_Finder false negatives
sherw:2392441850 - 244792010CDS
sherw:2382435595 - 244167610CDS
 
NC_003198 Salmonella enterica subsp. enterica serovar Typhi str. CT18 - 4809037bp  Go to Prophinder
sherw:1992760475 - 276877110CDS
prophinder:343352760910 - 27687719CDS9 overlapping CDS - Eval: 7e-26
phage_finder:165552759379 - 277408012CDS10 overlapping CDS - Eval: 1.9e-28
 
sherw:2014473973 - 450727044CDS
prophinder:343484472479 - 450727045CDS44 overlapping CDS - Eval: 2.3e-118
 
sherw:1981008747 - 105275565CDS
prophinder:343521008747 - 105126663CDS63 overlapping CDS - Eval: 6.8e-161
phage_finder:165521008467 - 104519155CDS55 overlapping CDS - Eval: 5.7e-136
 
sherw:1973515470 - 354897546CDS
prophinder:343473515470 - 354897546CDS46 overlapping CDS - Eval: 8.2e-125
phage_finder:165563492650 - 354179958CDS38 overlapping CDS - Eval: 1.3e-82
 
sherw:2051888674 - 193355867CDS
prophinder:343541889471 - 193355867CDS67 overlapping CDS - Eval: 3.6e-173
phage_finder:165541879753 - 193364375CDS67 overlapping CDS - Eval: 1.9e-164
 
sherw:1964683853 - 469454512CDS
prophinder:343394683853 - 469490713CDS12 overlapping CDS - Eval: 8.1e-35
 
sherw:2041538899 - 157291952CDS
prophinder:343441547849 - 157291935CDS35 overlapping CDS - Eval: 1.4e-84
phage_finder:165531538899 - 157291952CDS52 overlapping CDS - Eval: 3.5e-140
 
Phage_Finder false negatives
sherw:2014473973 - 450727044CDS
sherw:1964683853 - 469454512CDS
 
False positives
phage_finder:165574506090 - 455631348CDS
 
NC_004337 Shigella flexneri 2a str. 301 - 4607203bp  Go to Prophinder
sherw:182238841 - 25137012CDS
prophinder:35273237461 - 25270517CDS12 overlapping CDS - Eval: 3.9e-32
 
sherw:1792049694 - 206639721CDS
prophinder:352822049694 - 206639721CDS21 overlapping CDS - Eval: 2e-61
phage_finder:165852029271 - 206678639CDS21 overlapping CDS - Eval: 3.4e-51
 
sherw:1771175319 - 118840814CDS
prophinder:352711174923 - 118840815CDS14 overlapping CDS - Eval: 1.3e-40
 
sherw:1861395280 - 142188436CDS
prophinder:352851390345 - 142188442CDS36 overlapping CDS - Eval: 1.1e-93
 
sherw:1801919854 - 194269725CDS
prophinder:352861917075 - 194479929CDS25 overlapping CDS - Eval: 8.6e-68
phage_finder:165841919854 - 196493447CDS25 overlapping CDS - Eval: 1.2e-59
 
sherw:1762683559 - 269894419CDS
prophinder:352792680811 - 269552417CDS14 overlapping CDS - Eval: 6.9e-35
phage_finder:165862684565 - 269692615CDS15 overlapping CDS - Eval: 1.6e-41
 
sherw:184311291 - 32807921CDS
prophinder:35274311291 - 31822912CDS12 overlapping CDS - Eval: 1.8e-30
phage_finder:16582311264 - 34015437CDS21 overlapping CDS - Eval: 7.1e-52
 
sherw:178696659 - 74773461CDS
prophinder:35291702133 - 74773454CDS54 overlapping CDS - Eval: 5.3e-135
phage_finder:16583696659 - 75073663CDS61 overlapping CDS - Eval: 8.6e-158
 
Prophinder false negatives
sherw:185899706 - 91866826CDS
sherw:1812227585 - 22355658CDS
 
Phage_Finder false negatives
sherw:185899706 - 91866826CDS
sherw:1771175319 - 118840814CDS
sherw:1861395280 - 142188436CDS
sherw:182238841 - 25137012CDS
sherw:1812227585 - 22355658CDS
 
NC_002967 Treponema denticola ATCC 35405 - 2843201bp  Go to Prophinder
sherw:821169950 - 120241133CDS
phage_finder:166721164700 - 120263541CDS33 overlapping CDS - Eval: 1e-85
 
Prophinder false negatives
sherw:821169950 - 120241133CDS
 
NC_003116 Neisseria meningitidis Z2491 - 2184406bp  Go to Prophinder
sherw:2181207416 - 123626048CDS
prophinder:337681221378 - 123409611CDS11 overlapping CDS - Eval: 1.3e-22
phage_finder:164771208979 - 123577943CDS43 overlapping CDS - Eval: 2.2e-112
 
sherw:2191768546 - 180751562CDS
prophinder:337721773127 - 179340726CDS26 overlapping CDS - Eval: 1.7e-57
phage_finder:164781769385 - 180751561CDS61 overlapping CDS - Eval: 2.7e-159
 
Prophinder false negatives
sherw:2201131796 - 113889915CDS
 
Phage_Finder false negatives
sherw:2201131796 - 113889915CDS
 
NC_003030 Clostridium acetobutylicum ATCC 824 - 3940880bp  Go to Prophinder
sherw:1021277643 - 134678983CDS
phage_finder:163611270462 - 1372383126CDS83 overlapping CDS - Eval: 7.2e-176
 
sherw:1012024020 - 207425477CDS
prophinder:339232012657 - 206977288CDS72 overlapping CDS - Eval: 9.1e-160
phage_finder:163622014074 - 2088146104CDS77 overlapping CDS - Eval: 5e-172
 
Prophinder false negatives
sherw:1021277643 - 134678983CDS
 
NC_002737 Streptococcus pyogenes M1 GAS - 1852441bp  Go to Prophinder
sherw:491773458 - 178282213CDS
prophinder:351281773458 - 178282213CDS13 overlapping CDS - Eval: 7.1e-39
 
sherw:51778642 - 82059957CDS
prophinder:35130778642 - 81891255CDS55 overlapping CDS - Eval: 9.4e-143
phage_finder:16639778526 - 82101057CDS57 overlapping CDS - Eval: 7.2e-152
 
sherw:50527569 - 57188751CDS
prophinder:35125529631 - 56851346CDS46 overlapping CDS - Eval: 1.9e-118
phage_finder:16638529591 - 57050948CDS48 overlapping CDS - Eval: 2.2e-126
 
sherw:481192854 - 122254944CDS
prophinder:351271191309 - 122291247CDS44 overlapping CDS - Eval: 8.3e-116
phage_finder:166401189125 - 122265448CDS44 overlapping CDS - Eval: 9.2e-116
 
Phage_Finder false negatives
sherw:491773458 - 178282213CDS
 
NC_004431 Escherichia coli CFT073 - 5231428bp  Go to Prophinder
sherw:1051397370 - 145223183CDS
prophinder:324251397370 - 144563573CDS73 overlapping CDS - Eval: 5e-174
phage_finder:163951397105 - 145228284CDS83 overlapping CDS - Eval: 6.1e-208
 
sherw:1033019963 - 306531561CDS
prophinder:324233019963 - 306531561CDS61 overlapping CDS - Eval: 1.1e-159
phage_finder:163963018510 - 306712664CDS61 overlapping CDS - Eval: 1.8e-156
 
sherw:1101327053 - 137282077CDS
prophinder:324171338915 - 137105849CDS49 overlapping CDS - Eval: 4.8e-111
 
sherw:104909332 - 94227348CDS
prophinder:32416909332 - 94227348CDS48 overlapping CDS - Eval: 1.4e-129
phage_finder:16394908948 - 94547951CDS48 overlapping CDS - Eval: 2.2e-126
 
Prophinder false negatives
sherw:1084923133 - 492962815CDS
sherw:1071378215 - 138895225CDS
sherw:1091169792 - 122872955CDS
 
Phage_Finder false negatives
sherw:1084923133 - 492962815CDS
sherw:1101327053 - 137282077CDS
sherw:1071378215 - 138895225CDS
sherw:1091169792 - 122872955CDS
 
NC_004116 Streptococcus agalactiae 2603V/R - 2160267bp  Go to Prophinder
sherw:153558254 - 59920763CDS
prophinder:33065558826 - 60059463CDS62 overlapping CDS - Eval: 2.3e-158
phage_finder:16633558767 - 59934562CDS62 overlapping CDS - Eval: 1.4e-161
 
sherw:1521833318 - 186711750CDS
prophinder:330641833318 - 185354725CDS25 overlapping CDS - Eval: 4.6e-58
prophinder:330631853657 - 186711725CDS25 overlapping CDS - Eval: 4.6e-58
phage_finder:166341833085 - 186718850CDS50 overlapping CDS - Eval: 1.9e-135
 
NC_002745 Staphylococcus aureus subsp. aureus N315 - 2814816bp  Go to Prophinder
sherw:1702005924 - 204952064CDS
prophinder:355772038017 - 204842018CDS18 overlapping CDS - Eval: 1.4e-37
prophinder:355782009768 - 202772019CDS19 overlapping CDS - Eval: 5.5e-40
prophinder:355792028465 - 203780419CDS19 overlapping CDS - Eval: 5.5e-40
phage_finder:166202005190 - 207244690CDS64 overlapping CDS - Eval: 1.9e-145
 
NC_002662 Lactococcus lactis subsp. lactis Il1403 - 2365589bp  Go to Prophinder
sherw:53502723 - 51374221CDS
prophinder:32534502723 - 51154217CDS17 overlapping CDS - Eval: 1.4e-46
 
sherw:521036642 - 107155860CDS
prophinder:325601036642 - 107155860CDS60 overlapping CDS - Eval: 2e-157
phage_finder:164501036339 - 110090295CDS60 overlapping CDS - Eval: 1e-132
 
sherw:561414112 - 145694963CDS
prophinder:325461439215 - 144643819CDS19 overlapping CDS - Eval: 3.8e-40
prophinder:325621416048 - 14226747CDS7 overlapping CDS - Eval: 7.1e-12
prophinder:325401446550 - 145694919CDS19 overlapping CDS - Eval: 3.8e-40
prophinder:325351422690 - 143514010CDS10 overlapping CDS - Eval: 7.9e-19
phage_finder:164511415289 - 145711661CDS61 overlapping CDS - Eval: 8.6e-158
 
sherw:5735516 - 4972727CDS
prophinder:3254935516 - 4972727CDS27 overlapping CDS - Eval: 1.9e-77
phage_finder:1644828825 - 5638239CDS27 overlapping CDS - Eval: 1.6e-68
 
sherw:55447236 - 48324455CDS
prophinder:32550451007 - 48324449CDS49 overlapping CDS - Eval: 1.8e-124
phage_finder:16449447143 - 48409456CDS55 overlapping CDS - Eval: 1.8e-145
 
sherw:542013685 - 202563522CDS
prophinder:325532011426 - 202563523CDS22 overlapping CDS - Eval: 8.9e-63
 
Phage_Finder false negatives
sherw:53502723 - 51374221CDS
sherw:542013685 - 202563522CDS
 
NC_005085 Chromobacterium violaceum ATCC 12472 - 4751080bp  Go to Prophinder
sherw:287353384 - 37282620CDS
prophinder:35018353384 - 45039796CDS20 overlapping CDS - Eval: 2.4e-38
 
sherw:288428568 - 45039726CDS
prophinder:35018353384 - 45039796CDS26 overlapping CDS - Eval: 1.7e-51
 
sherw:2892303969 - 233474242CDS
prophinder:350172300705 - 232678634CDS30 overlapping CDS - Eval: 1.6e-70
phage_finder:163602300705 - 233952856CDS42 overlapping CDS - Eval: 2.1e-103
 
Phage_Finder false negatives
sherw:287353384 - 37282620CDS
sherw:288428568 - 45039726CDS
 
False positives
phage_finder:163591561058 - 157771711CDS
phage_finder:16358676267 - 68456610CDS
 
NC_002516 Pseudomonas aeruginosa PAO1 - 6264404bp  Go to Prophinder
sherw:41672777 - 68922122CDS
prophinder:33571673191 - 796776118CDS21 overlapping CDS - Eval: 4.2e-37
 
sherw:42689236 - 70252915CDS
prophinder:33571673191 - 796776118CDS15 overlapping CDS - Eval: 4.1e-26
 
Phage_Finder false negatives
sherw:41672777 - 68922122CDS
sherw:42689236 - 70252915CDS
 
False positives
phage_finder:16502785311 - 79774715CDS
 
NC_000964 Bacillus subtilis subsp. subtilis str. 168 - 4214630bp  Go to Prophinder
sherw:462151284 - 2285604185CDS
prophinder:344212212279 - 223186019CDS19 overlapping CDS - Eval: 2.4e-30
prophinder:344252245852 - 228560435CDS35 overlapping CDS - Eval: 4.5e-60
prophinder:344322151284 - 217374750CDS50 overlapping CDS - Eval: 1.4e-88
prophinder:344272173783 - 220695450CDS50 overlapping CDS - Eval: 1.4e-88
phage_finder:163332151229 - 2285644185CDS185 overlapping CDS - Eval: 0
 
sherw:432666111 - 270058246CDS
prophinder:344202682111 - 269690219CDS19 overlapping CDS - Eval: 2.6e-43
phage_finder:163342656042 - 269846956CDS43 overlapping CDS - Eval: 3.7e-102
 
sherw:471320640 - 134749431CDS
prophinder:344221313763 - 134749440CDS31 overlapping CDS - Eval: 2.4e-79
phage_finder:163321313763 - 135672548CDS31 overlapping CDS - Eval: 6.3e-76
 
Prophinder false negatives
sherw:452055488 - 206404411CDS
 
Phage_Finder false negatives
sherw:452055488 - 206404411CDS
 
False positives
phage_finder:16331528923 - 54949324CDS
 
NC_003366 Clostridium perfringens str. 13 - 3031430bp  Go to Prophinder
sherw:1571298199 - 132780038CDS
prophinder:337511312560 - 133168519CDS17 overlapping CDS - Eval: 1.2e-37
phage_finder:163631303501 - 133907742CDS30 overlapping CDS - Eval: 3.1e-68
 
False positives
prophinder:33750776014 - 79146711CDS
 
NC_003485 Streptococcus pyogenes MGAS8232 - 1895017bp  Go to Prophinder
sherw:911206360 - 124141656CDS
prophinder:326981208355 - 124141653CDS53 overlapping CDS - Eval: 7.1e-137
phage_finder:166601206171 - 124152256CDS56 overlapping CDS - Eval: 1.5e-149
 
sherw:931041280 - 108773969CDS
prophinder:326971043703 - 108640164CDS64 overlapping CDS - Eval: 2.1e-159
phage_finder:166591041142 - 108788069CDS69 overlapping CDS - Eval: 3.6e-179
 
sherw:92293882 - 33271453CDS
prophinder:32693308140 - 33143527CDS27 overlapping CDS - Eval: 1.9e-62
prophinder:32694293882 - 30798024CDS24 overlapping CDS - Eval: 1.3e-54
phage_finder:16657293804 - 382800107CDS53 overlapping CDS - Eval: 1.9e-111
 
sherw:901451844 - 149337356CDS
prophinder:326951455820 - 148944647CDS47 overlapping CDS - Eval: 2.6e-117
phage_finder:166611441660 - 149355867CDS56 overlapping CDS - Eval: 1.9e-137
 
sherw:89578093 - 61876560CDS
prophinder:32696578093 - 61712158CDS58 overlapping CDS - Eval: 1.3e-149
phage_finder:16658578053 - 61912060CDS60 overlapping CDS - Eval: 8.7e-159
 
NC_005362 Lactobacillus johnsonii NCC 533 - 1992676bp  Go to Prophinder
sherw:1111292553 - 133037750CDS
prophinder:335601294097 - 132724543CDS43 overlapping CDS - Eval: 1.3e-109
phage_finder:164451292072 - 133048150CDS50 overlapping CDS - Eval: 1.9e-135
 
sherw:112327894 - 36779146CDS
prophinder:33559332205 - 36714739CDS39 overlapping CDS - Eval: 4e-100
phage_finder:16444327838 - 36787346CDS46 overlapping CDS - Eval: 6.8e-126
 
NC_005126 Photorhabdus luminescens subsp. laumondii TTO1 - 5688987bp  Go to Prophinder
sherw:384006891 - 405669064CDS
prophinder:331704006891 - 407628294CDS64 overlapping CDS - Eval: 6e-142
phage_finder:165004007219 - 4094743122CDS63 overlapping CDS - Eval: 2.8e-128
 
sherw:303409531 - 3537385164CDS
prophinder:331613508362 - 353324326CDS26 overlapping CDS - Eval: 9.7e-45
prophinder:331653409531 - 345601975CDS75 overlapping CDS - Eval: 7.1e-143
prophinder:331493459819 - 34681498CDS8 overlapping CDS - Eval: 9.8e-11
phage_finder:164993409319 - 345625175CDS75 overlapping CDS - Eval: 1.5e-144
 
sherw:2910251 - 2999927CDS
prophinder:3315910251 - 2999927CDS27 overlapping CDS - Eval: 1.9e-77
phage_finder:1649810251 - 4135540CDS27 overlapping CDS - Eval: 4.8e-68
 
sherw:31132320 - 18039441CDS
prophinder:33157168154 - 1799697CDS7 overlapping CDS - Eval: 2.9e-13
 
Prophinder false negatives
sherw:335175988 - 519058915CDS
sherw:282800483 - 284850736CDS
sherw:363774756 - 389217364CDS
sherw:274190163 - 424279134CDS
sherw:324340686 - 438913437CDS
sherw:392088101 - 210127210CDS
sherw:352552735 - 257394020CDS
sherw:265201181 - 522881525CDS
sherw:242955621 - 299166137CDS
sherw:372331853 - 2466741115CDS
sherw:341267570 - 1617919231CDS
 
Phage_Finder false negatives
sherw:335175988 - 519058915CDS
sherw:282800483 - 284850736CDS
sherw:363774756 - 389217364CDS
sherw:274190163 - 424279134CDS
sherw:324340686 - 438913437CDS
sherw:392088101 - 210127210CDS
sherw:352552735 - 257394020CDS
sherw:265201181 - 522881525CDS
sherw:242955621 - 299166137CDS
sherw:31132320 - 18039441CDS
sherw:372331853 - 2466741115CDS
sherw:341267570 - 1617919231CDS
 
False positives
prophinder:331513955228 - 39635288CDS
prophinder:331721987183 - 206473162CDS
prophinder:331554086061 - 40927079CDS
 
NC_003923 Staphylococcus aureus subsp. aureus MW2 - 2820462bp  Go to Prophinder
sherw:1501529381 - 157300563CDS
prophinder:341441531688 - 157685964CDS61 overlapping CDS - Eval: 8.8e-152
 
sherw:1512046605 - 208874958CDS
prophinder:341452046605 - 208595255CDS55 overlapping CDS - Eval: 1.8e-141
phage_finder:166162035775 - 208887571CDS58 overlapping CDS - Eval: 2e-140
 
Phage_Finder false negatives
sherw:1501529381 - 157300563CDS
 
False positives
prophinder:34143839705 - 86646228CDS
 
NC_004631 Salmonella enterica subsp. enterica serovar Typhi Ty2 - 4791961bp  Go to Prophinder
sherw:1171314607 - 1441766142CDS
prophinder:342421408218 - 143281631CDS31 overlapping CDS - Eval: 1.6e-56
phage_finder:165471408218 - 144289249CDS48 overlapping CDS - Eval: 1e-90
 
sherw:1222735202 - 275462821CDS
prophinder:342432735202 - 275462821CDS21 overlapping CDS - Eval: 2e-61
phage_finder:165492734604 - 275993722CDS21 overlapping CDS - Eval: 1.2e-60
 
sherw:1181928058 - 197233064CDS
prophinder:342471930272 - 197233062CDS62 overlapping CDS - Eval: 1.2e-158
phage_finder:165481927739 - 197237964CDS64 overlapping CDS - Eval: 6.5e-168
 
sherw:1194458029 - 449085642CDS
prophinder:342454456072 - 449085644CDS42 overlapping CDS - Eval: 3.3e-112
 
sherw:1213501128 - 353807648CDS
prophinder:342443501128 - 353463545CDS45 overlapping CDS - Eval: 3.5e-118
phage_finder:165503490720 - 352760346CDS37 overlapping CDS - Eval: 2.1e-84
 
Prophinder false negatives
sherw:1204671630 - 46780349CDS
 
Phage_Finder false negatives
sherw:1204671630 - 46780349CDS
sherw:1194458029 - 449085642CDS
 
False positives
phage_finder:165514489676 - 453921545CDS
 
NC_003143 Yersinia pestis CO92 - 4653728bp  Go to Prophinder
sherw:92363019 - 241309856CDS
prophinder:351472365343 - 240306446CDS46 overlapping CDS - Eval: 2.9e-114
phage_finder:166942364324 - 241032554CDS54 overlapping CDS - Eval: 1.1e-141
 
sherw:6964013 - 9713118CDS
prophinder:35141959426 - 97131113CDS8 overlapping CDS - Eval: 1.2e-20
 
sherw:41392489 - 141652428CDS
prophinder:351421399772 - 141122014CDS14 overlapping CDS - Eval: 3.5e-34
 
sherw:71233128 - 124340513CDS
phage_finder:166931224076 - 124569023CDS13 overlapping CDS - Eval: 3.3e-33
 
Prophinder false negatives
sherw:102554373 - 256320313CDS
sherw:71233128 - 124340513CDS
sherw:52115626 - 212260314CDS
 
Phage_Finder false negatives
sherw:6964013 - 9713118CDS
sherw:41392489 - 141652428CDS
sherw:102554373 - 256320313CDS
sherw:52115626 - 212260314CDS
 
NC_004668 Enterococcus faecalis V583 - 3218031bp  Go to Prophinder
sherw:15289354 - 32618553CDS
prophinder:35093289354 - 32618553CDS53 overlapping CDS - Eval: 2.6e-141
phage_finder:16384289300 - 32636253CDS53 overlapping CDS - Eval: 1.5e-142
 
sherw:122700666 - 273680854CDS
prophinder:350902703543 - 273468649CDS49 overlapping CDS - Eval: 1.9e-125
phage_finder:163882700412 - 273693154CDS54 overlapping CDS - Eval: 6.9e-145
 
sherw:181398097 - 144384370CDS
prophinder:350951398097 - 144384370CDS70 overlapping CDS - Eval: 8.1e-180
phage_finder:163851415824 - 145964453CDS36 overlapping CDS - Eval: 9.2e-68
 
sherw:141923000 - 196248546CDS
prophinder:350891925423 - 196248543CDS43 overlapping CDS - Eval: 2e-113
phage_finder:163861922618 - 196255946CDS46 overlapping CDS - Eval: 6.8e-126
 
sherw:161245337 - 125996518CDS
prophinder:350801245337 - 125996518CDS18 overlapping CDS - Eval: 3.8e-53
 
sherw:132004910 - 204814662CDS
prophinder:350852030238 - 204814634CDS34 overlapping CDS - Eval: 7.4e-78
phage_finder:163872004742 - 204827162CDS62 overlapping CDS - Eval: 2.3e-163
 
Prophinder false negatives
sherw:192817287 - 282955420CDS
 
Phage_Finder false negatives
sherw:192817287 - 282955420CDS
sherw:161245337 - 125996518CDS
 
NC_003295 Ralstonia solanacearum GMI1000 - 3716413bp  Go to Prophinder
sherw:1231781995 - 182395353CDS
prophinder:338161800969 - 181887819CDS19 overlapping CDS - Eval: 7.4e-42
phage_finder:165261781780 - 182424053CDS53 overlapping CDS - Eval: 1.5e-142
 
sherw:126879632 - 93943754CDS
prophinder:33819879632 - 90930935CDS35 overlapping CDS - Eval: 1.2e-83
phage_finder:16523909375 - 94297521CDS18 overlapping CDS - Eval: 1.5e-36
 
sherw:1241003644 - 101847314CDS
phage_finder:16524994222 - 101863823CDS14 overlapping CDS - Eval: 2.7e-36
 
sherw:1282084602 - 212434653CDS
prophinder:338182092493 - 211557331CDS31 overlapping CDS - Eval: 4e-73
phage_finder:165272084443 - 212515753CDS53 overlapping CDS - Eval: 1.5e-142
 
Prophinder false negatives
sherw:1291591303 - 15989869CDS
sherw:1241003644 - 101847314CDS
sherw:1303486521 - 350555023CDS
sherw:1272049204 - 20560367CDS
sherw:1252684129 - 269578815CDS
 
Phage_Finder false negatives
sherw:1291591303 - 15989869CDS
sherw:1303486521 - 350555023CDS
sherw:1272049204 - 20560367CDS
sherw:1252684129 - 269578815CDS
 
False positives
phage_finder:165283430385 - 346803235CDS
phage_finder:165251647746 - 167115913CDS
 
NC_003155 Streptomyces avermitilis MA-4680 - 9025608bp  Go to Prophinder
sherw:1696670511 - 672144463CDS
prophinder:342306678303 - 669362517CDS17 overlapping CDS - Eval: 2.4e-35
phage_finder:166686667915 - 671196857CDS56 overlapping CDS - Eval: 4.7e-139
 
NC_004347 Shewanella oneidensis MR-1 - 4969803bp  Go to Prophinder
sherw:236669361 - 70390842CDS
prophinder:32437675979 - 70054730CDS30 overlapping CDS - Eval: 3.5e-75
phage_finder:16564669361 - 70964150CDS42 overlapping CDS - Eval: 1.9e-107
 
sherw:2353075409 - 312624974CDS
prophinder:324413107999 - 312335826CDS26 overlapping CDS - Eval: 5.4e-55
prophinder:324393076443 - 310799940CDS40 overlapping CDS - Eval: 3.6e-89
phage_finder:165663074590 - 312644275CDS74 overlapping CDS - Eval: 2.2e-188
 
sherw:2342788307 - 282283653CDS
prophinder:324382795964 - 282283639CDS39 overlapping CDS - Eval: 1.8e-95
phage_finder:165652788307 - 282561654CDS53 overlapping CDS - Eval: 8.3e-141
 
NC_004088 Yersinia pestis KIM - 4600755bp  Go to Prophinder
sherw:1622417129 - 245646742CDS
prophinder:336232407095 - 245646749CDS42 overlapping CDS - Eval: 3e-107
phage_finder:166952415479 - 245652343CDS42 overlapping CDS - Eval: 1.5e-114
 
sherw:1583389410 - 339975410CDS
prophinder:336213390110 - 340914418CDS9 overlapping CDS - Eval: 3.4e-21
phage_finder:166963389136 - 341073221CDS10 overlapping CDS - Eval: 1e-24
 
sherw:1603237524 - 325525223CDS
prophinder:336203236486 - 324774314CDS13 overlapping CDS - Eval: 1.1e-31
 
sherw:1613595228 - 36013438CDS
prophinder:336173595228 - 36013438CDS8 overlapping CDS - Eval: 8.9e-24
 
Prophinder false negatives
sherw:1592693615 - 270057613CDS
 
Phage_Finder false negatives
sherw:1603237524 - 325525223CDS
sherw:1613595228 - 36013438CDS
sherw:1592693615 - 270057613CDS
 
NC_004556 Xylella fastidiosa Temecula1 - 2519802bp  Go to Prophinder
sherw:213454017 - 46761122CDS
prophinder:34659454017 - 46761122CDS22 overlapping CDS - Eval: 3.9e-64
phage_finder:16688453721 - 46764222CDS22 overlapping CDS - Eval: 1e-64
 
sherw:2101161143 - 121790762CDS
prophinder:346561161143 - 119598833CDS33 overlapping CDS - Eval: 2.9e-75
prophinder:346631196130 - 121790729CDS29 overlapping CDS - Eval: 5e-65
phage_finder:166891181498 - 122797941CDS33 overlapping CDS - Eval: 4.2e-68
 
sherw:2081288547 - 1392763105CDS
prophinder:346641322272 - 13315419CDS9 overlapping CDS - Eval: 2.1e-14
prophinder:346601288023 - 131341030CDS29 overlapping CDS - Eval: 2.3e-55
prophinder:346571376468 - 139276322CDS22 overlapping CDS - Eval: 9.5e-42
phage_finder:166911379639 - 139309018CDS18 overlapping CDS - Eval: 9.5e-34
phage_finder:166901287845 - 133164853CDS52 overlapping CDS - Eval: 5.7e-108
 
sherw:2091847752 - 18555829CDS
prophinder:346711848608 - 18586598CDS6 overlapping CDS - Eval: 4.9e-14
 
sherw:2152005731 - 202042118CDS
prophinder:346512011241 - 20189287CDS7 overlapping CDS - Eval: 4.1e-16
 
sherw:2141117952 - 114262738CDS
prophinder:346541120075 - 113200517CDS17 overlapping CDS - Eval: 6.9e-40
 
Prophinder false negatives
sherw:2111550281 - 15561887CDS
 
Phage_Finder false negatives
sherw:2111550281 - 15561887CDS
sherw:2091847752 - 18555829CDS
sherw:2141117952 - 114262738CDS
sherw:2152005731 - 202042118CDS
 
False positives
phage_finder:166921848608 - 18555826CDS
 
NC_004741 Shigella flexneri 2a str. 2457T - 4599354bp  Go to Prophinder
sherw:227313843 - 32722314CDS
phage_finder:16576313783 - 32431910CDS10 overlapping CDS - Eval: 2.9e-27
 
sherw:2302021895 - 204434224CDS
prophinder:339482027802 - 204170917CDS17 overlapping CDS - Eval: 8.2e-45
phage_finder:165801992538 - 204461854CDS24 overlapping CDS - Eval: 5.5e-55
 
sherw:2321901037 - 192179324CDS
phage_finder:165791900980 - 195409353CDS24 overlapping CDS - Eval: 3.1e-55
 
sherw:233238511 - 25470020CDS
prophinder:33949240794 - 25603417CDS15 overlapping CDS - Eval: 2.4e-38
 
sherw:2261912634 - 192179310CDS
phage_finder:165791900980 - 195409353CDS10 overlapping CDS - Eval: 5.6e-20
 
sherw:222692891 - 70911826CDS
prophinder:33970698365 - 74389259CDS18 overlapping CDS - Eval: 3.7e-32
phage_finder:16577692891 - 74824170CDS26 overlapping CDS - Eval: 2e-56
 
sherw:2242678519 - 268751711CDS
prophinder:339552674398 - 268896817CDS11 overlapping CDS - Eval: 7.3e-29
phage_finder:165812678152 - 269037015CDS11 overlapping CDS - Eval: 3.6e-30
 
sherw:231710297 - 74612342CDS
prophinder:33970698365 - 74389259CDS41 overlapping CDS - Eval: 2.6e-96
phage_finder:16577692891 - 74824170CDS42 overlapping CDS - Eval: 9.9e-97
 
sherw:229897790 - 93067040CDS
prophinder:33957897993 - 92578230CDS30 overlapping CDS - Eval: 2.7e-76
 
sherw:2251177837 - 119159616CDS
prophinder:339521186255 - 11913017CDS7 overlapping CDS - Eval: 1.5e-16
phage_finder:165781177513 - 122512546CDS16 overlapping CDS - Eval: 5.5e-36
 
Prophinder false negatives
sherw:227313843 - 32722314CDS
sherw:2321901037 - 192179324CDS
sherw:2281614219 - 16206227CDS
sherw:2261912634 - 192179310CDS
sherw:2231100131 - 11059199CDS
 
Phage_Finder false negatives
sherw:2281614219 - 16206227CDS
sherw:233238511 - 25470020CDS
sherw:2231100131 - 11059199CDS
sherw:229897790 - 93067040CDS
 
False positives
prophinder:339732208343 - 221731710CDS
prophinder:339531886271 - 189984613CDS
 
NC_003997 Bacillus anthracis str. Ames - 5227293bp  Go to Prophinder
sherw:1153456916 - 350568566CDS
prophinder:345043453008 - 350550270CDS65 overlapping CDS - Eval: 8.4e-160
phage_finder:163063452803 - 353164596CDS66 overlapping CDS - Eval: 1.3e-147
 
sherw:1143745958 - 379104271CDS
prophinder:344963746587 - 377423934CDS34 overlapping CDS - Eval: 4.4e-75
prophinder:344943781824 - 378779014CDS14 overlapping CDS - Eval: 2.1e-27
phage_finder:163073751165 - 380532377CDS61 overlapping CDS - Eval: 2.8e-133
 
sherw:1134842149 - 485824024CDS
prophinder:344954849801 - 48582408CDS8 overlapping CDS - Eval: 6.6e-18
phage_finder:163084841710 - 485848924CDS24 overlapping CDS - Eval: 3.9e-70
 
sherw:116447387 - 48433957CDS
prophinder:34501447387 - 48213952CDS52 overlapping CDS - Eval: 2.3e-132
phage_finder:16305447283 - 48466457CDS57 overlapping CDS - Eval: 7.2e-152
 
NC_004578 Pseudomonas syringae pv. tomato str. DC3000 - 6397126bp  Go to Prophinder
sherw:3244515380 - 453037316CDS
prophinder:338564517028 - 455629944CDS16 overlapping CDS - Eval: 6.7e-36
 
sherw:320625118 - 64748318CDS
prophinder:33849632092 - 6391787CDS7 overlapping CDS - Eval: 4.1e-16
phage_finder:16515628136 - 65098020CDS16 overlapping CDS - Eval: 4.1e-42
 
sherw:3254543843 - 456349521CDS
prophinder:338564517028 - 455629944CDS10 overlapping CDS - Eval: 5.2e-15
phage_finder:165184542868 - 456358623CDS21 overlapping CDS - Eval: 1.4e-59
 
sherw:3223824683 - 386535245CDS
prophinder:338553824867 - 386769347CDS45 overlapping CDS - Eval: 2.2e-119
phage_finder:165163824685 - 386536845CDS45 overlapping CDS - Eval: 1.8e-123
 
Prophinder false negatives
sherw:3212252628 - 226499918CDS
 
Phage_Finder false negatives
sherw:3244515380 - 453037316CDS
sherw:3212252628 - 226499918CDS
 
False positives
phage_finder:165174445037 - 445868116CDS
 
NC_004567 Lactobacillus plantarum WCFS1 - 3308274bp  Go to Prophinder
sherw:166590128 - 63380460CDS
prophinder:33588590128 - 62838157CDS57 overlapping CDS - Eval: 5e-146
phage_finder:16446606331 - 64405936CDS29 overlapping CDS - Eval: 2.1e-59
 
sherw:1672204171 - 221834219CDS
prophinder:335822205185 - 221834217CDS17 overlapping CDS - Eval: 4.1e-48
 
sherw:1652161732 - 220382056CDS
prophinder:335872146749 - 220261269CDS55 overlapping CDS - Eval: 5.1e-130
phage_finder:164472162771 - 220406055CDS55 overlapping CDS - Eval: 1.8e-145
 
Prophinder false negatives
sherw:1682998563 - 300728013CDS
 
Phage_Finder false negatives
sherw:1682998563 - 300728013CDS
sherw:1672204171 - 221834219CDS
 
NC_004307 Bifidobacterium longum NCC2705 - 2256640bp  Go to Prophinder
sherw:1451298692 - 131286715CDS
phage_finder:163391295506 - 131300219CDS15 overlapping CDS - Eval: 1.6e-41
 
Prophinder false negatives
sherw:1451298692 - 131286715CDS
 
False positives
prophinder:33142708145 - 72222911CDS
 
NC_002695 Escherichia coli O157:H7 str. Sakai - 5498450bp  Go to Prophinder
sherw:692667460 - 271301658CDS
prophinder:328002670690 - 271198354CDS54 overlapping CDS - Eval: 5.2e-138
phage_finder:164102668007 - 271209656CDS56 overlapping CDS - Eval: 2.5e-146
 
sherw:77310806 - 32440518CDS
prophinder:32770310806 - 32189116CDS16 overlapping CDS - Eval: 2.4e-45
 
sherw:72892240 - 92929249CDS
prophinder:32771892240 - 92560145CDS45 overlapping CDS - Eval: 4.3e-117
phage_finder:16402892240 - 92560145CDS45 overlapping CDS - Eval: 3.8e-118
 
sherw:782896151 - 294374772CDS
prophinder:328042896151 - 294374772CDS72 overlapping CDS - Eval: 3.2e-184
phage_finder:164112895905 - 294380572CDS72 overlapping CDS - Eval: 7.7e-186
 
sherw:801921472 - 197001466CDS
prophinder:327781933798 - 197001445CDS45 overlapping CDS - Eval: 1.8e-105
prophinder:327651921472 - 193200617CDS17 overlapping CDS - Eval: 6e-35
phage_finder:164071940750 - 198736748CDS36 overlapping CDS - Eval: 1e-71
 
sherw:651594751 - 160918427CDS
prophinder:327421601213 - 160888912CDS12 overlapping CDS - Eval: 1.1e-28
phage_finder:164051541478 - 1687839189CDS27 overlapping CDS - Eval: 1.5e-45
 
sherw:762211826 - 225416158CDS
prophinder:327802211555 - 224470642CDS41 overlapping CDS - Eval: 7.9e-97
phage_finder:164082189516 - 224056373CDS34 overlapping CDS - Eval: 2.7e-59
 
sherw:793480256 - 350503925CDS
prophinder:327913480256 - 349019615CDS15 overlapping CDS - Eval: 3.7e-38
phage_finder:164123475789 - 349495224CDS19 overlapping CDS - Eval: 1.4e-46
 
sherw:705041093 - 507946958CDS
prophinder:327835050313 - 507796036CDS36 overlapping CDS - Eval: 1.1e-84
phage_finder:164135041814 - 507946957CDS57 overlapping CDS - Eval: 4.2e-150
 
sherw:711161297 - 121064166CDS
prophinder:327721174631 - 120912644CDS44 overlapping CDS - Eval: 9.3e-103
phage_finder:164031161091 - 121080566CDS66 overlapping CDS - Eval: 2e-172
 
sherw:741541626 - 158984266CDS
prophinder:327941541626 - 157904158CDS58 overlapping CDS - Eval: 4.2e-143
phage_finder:164051541478 - 1687839189CDS66 overlapping CDS - Eval: 1.5e-120
 
sherw:681245217 - 130818292CDS
prophinder:328021246040 - 130818291CDS91 overlapping CDS - Eval: 5.8e-223
phage_finder:164041245903 - 131640899CDS91 overlapping CDS - Eval: 9.7e-214
 
sherw:63300072 - 31023814CDS
prophinder:32732300072 - 31023814CDS14 overlapping CDS - Eval: 8.7e-42
phage_finder:16401300012 - 31064414CDS14 overlapping CDS - Eval: 3.3e-42
 
sherw:731618212 - 166539459CDS
prophinder:327951618212 - 165301144CDS44 overlapping CDS - Eval: 2e-106
phage_finder:164051541478 - 1687839189CDS59 overlapping CDS - Eval: 9.8e-107
 
sherw:661756865 - 180421954CDS
prophinder:327771763879 - 180051442CDS42 overlapping CDS - Eval: 1.2e-103
phage_finder:164061757453 - 181568061CDS53 overlapping CDS - Eval: 2.4e-131
 
sherw:752593128 - 261202628CDS
prophinder:327902598416 - 261202615CDS15 overlapping CDS - Eval: 4.3e-37
phage_finder:164092592901 - 261414128CDS28 overlapping CDS - Eval: 9.4e-81
 
sherw:672158314 - 220391466CDS
prophinder:327792160832 - 219557346CDS46 overlapping CDS - Eval: 3.3e-108
phage_finder:164082189516 - 224056373CDS27 overlapping CDS - Eval: 6.3e-40
 
Prophinder false negatives
sherw:643193144 - 32000857CDS
 
Phage_Finder false negatives
sherw:77310806 - 32440518CDS
sherw:643193144 - 32000857CDS
 
False positives
prophinder:327895358407 - 539646720CDS
 
NC_003210 Listeria monocytogenes EGD-e - 2944528bp  Go to Prophinder
sherw:1472361897 - 240024358CDS
prophinder:331372360908 - 240323563CDS58 overlapping CDS - Eval: 5.2e-146
phage_finder:164582358515 - 240260364CDS58 overlapping CDS - Eval: 2.6e-146
 
sherw:146120654 - 13138017CDS
prophinder:33131120654 - 13138017CDS17 overlapping CDS - Eval: 2.4e-50
 
Phage_Finder false negatives
sherw:146120654 - 13138017CDS
 
NC_002678 Mesorhizobium loti MAFF303099 - 7036071bp  Go to Prophinder
sherw:1336587513 - 65957567CDS
prophinder:333036575295 - 662343858CDS7 overlapping CDS - Eval: 3.8e-12
phage_finder:164656575119 - 660524639CDS7 overlapping CDS - Eval: 1e-13
 
sherw:1316975631 - 701159145CDS
phage_finder:164666984118 - 701685536CDS31 overlapping CDS - Eval: 9.3e-72
 
Prophinder false negatives
sherw:132313639 - 35945752CDS
sherw:1316975631 - 701159145CDS
 
Phage_Finder false negatives
sherw:132313639 - 35945752CDS
 
False positives
prophinder:333004878385 - 489037712CDS
 
NC_002488 Xylella fastidiosa 9a5c - 2679306bp  Go to Prophinder
sherw:3131585980 - 163105670CDS
prophinder:337181599063 - 162789844CDS44 overlapping CDS - Eval: 5.7e-101
phage_finder:166861585873 - 163068769CDS69 overlapping CDS - Eval: 2.6e-177
 
sherw:3161514347 - 154107544CDS
prophinder:337171521506 - 154014228CDS28 overlapping CDS - Eval: 2e-68
phage_finder:166851514046 - 154902153CDS44 overlapping CDS - Eval: 2.1e-111
 
sherw:3182361812 - 240426852CDS
prophinder:337112395064 - 24042689CDS9 overlapping CDS - Eval: 2.6e-17
prophinder:337202361085 - 238725029CDS28 overlapping CDS - Eval: 5.9e-64
phage_finder:166872369149 - 240457044CDS44 overlapping CDS - Eval: 3.5e-112
 
sherw:315489619 - 53013852CDS
prophinder:33747487057 - 53269661CDS52 overlapping CDS - Eval: 9.6e-129
phage_finder:16683488229 - 53013856CDS52 overlapping CDS - Eval: 1.3e-134
 
sherw:312649115 - 69037556CDS
prophinder:33716664858 - 69037530CDS30 overlapping CDS - Eval: 2.1e-69
prophinder:33723649115 - 6584709CDS9 overlapping CDS - Eval: 5.3e-17
phage_finder:16684648982 - 70299671CDS56 overlapping CDS - Eval: 1.4e-134
 
sherw:3112177071 - 21831358CDS
prophinder:337412177071 - 218931816CDS8 overlapping CDS - Eval: 1.2e-19
 
sherw:3172008224 - 202237220CDS
prophinder:337222008987 - 202237218CDS18 overlapping CDS - Eval: 7.1e-51
 
Phage_Finder false negatives
sherw:3112177071 - 21831358CDS
sherw:3172008224 - 202237220CDS
 
False positives
prophinder:337241775629 - 179010824CDS
 
NC_003212 Listeria innocua Clip11262 - 3011208bp  Go to Prophinder
sherw:244155931 - 16666117CDS
prophinder:34915155931 - 16666117CDS17 overlapping CDS - Eval: 2.4e-50
 
sherw:24678505 - 11425055CDS
prophinder:3493676209 - 11425057CDS55 overlapping CDS - Eval: 9.4e-143
phage_finder:1645376060 - 11559958CDS55 overlapping CDS - Eval: 9.9e-143
 
sherw:2471713958 - 176208969CDS
prophinder:349241713958 - 174737947CDS47 overlapping CDS - Eval: 2e-109
prophinder:349301747616 - 176208922CDS22 overlapping CDS - Eval: 2.3e-46
phage_finder:164551708735 - 176242573CDS69 overlapping CDS - Eval: 4e-173
 
sherw:2492591482 - 262580746CDS
prophinder:349212620331 - 26258079CDS9 overlapping CDS - Eval: 7.8e-18
prophinder:349352587880 - 262032041CDS37 overlapping CDS - Eval: 7.4e-89
phage_finder:164572587434 - 262592250CDS46 overlapping CDS - Eval: 1.6e-120
 
sherw:2481246563 - 129423566CDS
prophinder:349221245851 - 126237225CDS24 overlapping CDS - Eval: 2.6e-50
prophinder:349291262385 - 129423542CDS42 overlapping CDS - Eval: 2.2e-97
phage_finder:164541246414 - 130452979CDS66 overlapping CDS - Eval: 5.2e-158
 
sherw:2452407382 - 244589153CDS
prophinder:349172406902 - 242093714CDS13 overlapping CDS - Eval: 8.3e-26
prophinder:349132433733 - 244374016CDS16 overlapping CDS - Eval: 2.4e-34
phage_finder:164562404858 - 244599356CDS53 overlapping CDS - Eval: 4.2e-138
 
Phage_Finder false negatives
sherw:244155931 - 16666117CDS
 
NC_004310 Brucella suis 1330 - 2107794bp  Go to Prophinder
sherw:148578085 - 58487910CDS
prophinder:33241578578 - 5848799CDS9 overlapping CDS - Eval: 7e-26
phage_finder:16344579764 - 59372917CDS8 overlapping CDS - Eval: 5e-18
 
NC_003197 Salmonella typhimurium LT2 - 4857432bp  Go to Prophinder
sherw:961098228 - 114371454CDS
prophinder:348301098228 - 114221351CDS51 overlapping CDS - Eval: 3e-132
phage_finder:165591098179 - 114403454CDS54 overlapping CDS - Eval: 6.9e-145
 
sherw:972330961 - 234521715CDS
prophinder:348112330961 - 234055611CDS11 overlapping CDS - Eval: 8.1e-30
phage_finder:165602326826 - 234471118CDS14 overlapping CDS - Eval: 1.5e-37
 
sherw:99962612 - 100651744CDS
prophinder:34818962612 - 100332641CDS41 overlapping CDS - Eval: 1.3e-108
phage_finder:16558962430 - 100449642CDS42 overlapping CDS - Eval: 3.4e-113
 
sherw:942844427 - 287923346CDS
prophinder:348172844427 - 287784045CDS45 overlapping CDS - Eval: 9.3e-121
phage_finder:165622844265 - 287800445CDS45 overlapping CDS - Eval: 8.2e-122
 
sherw:1004417918 - 443833524CDS
prophinder:348144419834 - 443539115CDS15 overlapping CDS - Eval: 1.5e-38
phage_finder:165634417918 - 443833524CDS24 overlapping CDS - Eval: 3.9e-70
 
sherw:982728976 - 277681653CDS
prophinder:348212733337 - 277003742CDS42 overlapping CDS - Eval: 2.7e-104
phage_finder:165612728534 - 277706353CDS53 overlapping CDS - Eval: 1.5e-142
 
Prophinder false negatives
sherw:952042050 - 205990918CDS
 
Phage_Finder false negatives
sherw:952042050 - 205990918CDS
 
NC_002570 Bacillus halodurans C-125 - 4202352bp  Go to Prophinder
sherw:863617919 - 365212244CDS
prophinder:344773617919 - 365212244CDS44 overlapping CDS - Eval: 5.1e-120
phage_finder:163203617735 - 365228044CDS44 overlapping CDS - Eval: 4.7e-121
 
sherw:851028696 - 103916011CDS
prophinder:344731028696 - 104307513CDS11 overlapping CDS - Eval: 4.6e-31
 
sherw:8410970 - 2216110CDS
prophinder:344824177128 - 7397382CDS10 overlapping CDS - Eval: 1.3e-17
 
Prophinder false negatives
sherw:871381009 - 13843487CDS
 
Phage_Finder false negatives
sherw:871381009 - 13843487CDS
sherw:851028696 - 103916011CDS
sherw:8410970 - 2216110CDS
 
NC_000907 Haemophilus influenzae Rd KW20 - 1830138bp  Go to Prophinder
sherw:1881559962 - 159427545CDS
prophinder:349001571077 - 159337426CDS26 overlapping CDS - Eval: 2e-62
phage_finder:164361559962 - 160249750CDS45 overlapping CDS - Eval: 3.8e-117
 
sherw:1871499076 - 151307318CDS
prophinder:348961499076 - 150960113CDS13 overlapping CDS - Eval: 6.1e-35
phage_finder:164351498816 - 151322419CDS18 overlapping CDS - Eval: 2.3e-52
 
False positives
phage_finder:164371630955 - 16382886CDS
 
NC_004557 Clostridium tetani E88 - 2799251bp  Go to Prophinder
sherw:221138054 - 118100343CDS
prophinder:338381138054 - 116777232CDS32 overlapping CDS - Eval: 1.4e-80
phage_finder:163641138054 - 116777232CDS32 overlapping CDS - Eval: 2.3e-81
 
sherw:202242455 - 228138742CDS
prophinder:338362263804 - 228138719CDS19 overlapping CDS - Eval: 2.8e-44
phage_finder:163662243139 - 228138140CDS40 overlapping CDS - Eval: 2.5e-108
 
sherw:211663821 - 169630228CDS
prophinder:338371657784 - 169527132CDS27 overlapping CDS - Eval: 1.1e-70
phage_finder:163651663516 - 169648928CDS28 overlapping CDS - Eval: 9.4e-81
 
NC_004070 Streptococcus pyogenes MGAS315 - 1900521bp  Go to Prophinder
sherw:3001230304 - 127181564CDS
prophinder:335391230304 - 127181564CDS64 overlapping CDS - Eval: 1.8e-166
phage_finder:166491221158 - 127198972CDS64 overlapping CDS - Eval: 7.8e-158
 
sherw:2961313282 - 135125055CDS
prophinder:335341314561 - 135125053CDS53 overlapping CDS - Eval: 3.8e-138
phage_finder:166501313194 - 135139955CDS55 overlapping CDS - Eval: 3.2e-147
 
sherw:301977738 - 101819359CDS
prophinder:33531978733 - 101819358CDS58 overlapping CDS - Eval: 4.4e-151
phage_finder:16647977267 - 101833460CDS59 overlapping CDS - Eval: 1e-154
 
sherw:298749213 - 78817656CDS
prophinder:33506758443 - 76353512CDS12 overlapping CDS - Eval: 3.5e-24
prophinder:33515749213 - 75844312CDS12 overlapping CDS - Eval: 3.5e-24
phage_finder:16646749180 - 78790055CDS55 overlapping CDS - Eval: 1.8e-145
 
sherw:2991137743 - 117186752CDS
prophinder:335321139031 - 117223151CDS50 overlapping CDS - Eval: 1.8e-129
phage_finder:166481137554 - 117197352CDS52 overlapping CDS - Eval: 3.5e-140
 
sherw:2971410725 - 145045851CDS
prophinder:335271412441 - 145045849CDS49 overlapping CDS - Eval: 7.8e-129
phage_finder:166511410657 - 145048451CDS51 overlapping CDS - Eval: 7.9e-138
 
NC_002978 Wolbachia endosymbiont of Drosophila melanogaster - 1267782bp  Go to Prophinder
sherw:241551654 - 5586259CDS
prophinder:32385542719 - 63829484CDS9 overlapping CDS - Eval: 2.6e-15
phage_finder:16677543609 - 62822268CDS9 overlapping CDS - Eval: 1.7e-16
 
sherw:242623343 - 63453713CDS
prophinder:32385542719 - 63829484CDS13 overlapping CDS - Eval: 4.4e-24
 
sherw:243245829 - 27522531CDS
prophinder:32380231348 - 26405730CDS20 overlapping CDS - Eval: 2.8e-43
phage_finder:16676231382 - 26905235CDS26 overlapping CDS - Eval: 2.1e-62
 
sherw:240567453 - 58256118CDS
prophinder:32385542719 - 63829484CDS18 overlapping CDS - Eval: 3.6e-35
phage_finder:16677543609 - 62822268CDS18 overlapping CDS - Eval: 1.5e-37
 
Phage_Finder false negatives
sherw:242623343 - 63453713CDS
 
NC_004722 Bacillus cereus ATCC 14579 - 5411809bp  Go to Prophinder
sherw:2721805567 - 186603671CDS
prophinder:332261804060 - 186603673CDS71 overlapping CDS - Eval: 1.3e-178
phage_finder:163141803172 - 186642374CDS71 overlapping CDS - Eval: 8.3e-179
 
sherw:2732531805 - 256509344CDS
prophinder:332182535143 - 254398013CDS13 overlapping CDS - Eval: 3.7e-28
prophinder:332162547592 - 256509319CDS19 overlapping CDS - Eval: 8.8e-44
phage_finder:163162529953 - 256644946CDS44 overlapping CDS - Eval: 4.9e-118
 
sherw:2752355784 - 236931114CDS
phage_finder:163152348917 - 236358516CDS10 overlapping CDS - Eval: 2.3e-23
 
sherw:2703660466 - 366882511CDS
prophinder:332173656256 - 366882516CDS11 overlapping CDS - Eval: 2.6e-29
 
Prophinder false negatives
sherw:2752355784 - 236931114CDS
 
Phage_Finder false negatives
sherw:2703660466 - 366882511CDS
 
NC_002655 Escherichia coli O157:H7 EDL933 - 5528445bp  Go to Prophinder
sherw:2591678706 - 169373722CDS
prophinder:354951685186 - 169286210CDS10 overlapping CDS - Eval: 4e-24
phage_finder:164181678525 - 176171099CDS22 overlapping CDS - Eval: 5.8e-43
 
sherw:252310756 - 32311217CDS
prophinder:35499310756 - 32189215CDS15 overlapping CDS - Eval: 1.6e-42
 
sherw:268892845 - 93094342CDS
prophinder:35500892845 - 92725239CDS39 overlapping CDS - Eval: 8.7e-104
phage_finder:16415892627 - 93592946CDS42 overlapping CDS - Eval: 5.8e-111
 
sherw:2672966382 - 301501464CDS
prophinder:355292966382 - 301501464CDS64 overlapping CDS - Eval: 1.8e-166
phage_finder:164242966136 - 301507264CDS64 overlapping CDS - Eval: 6.5e-168
 
sherw:2611330857 - 139192368CDS
prophinder:355251330857 - 139192368CDS68 overlapping CDS - Eval: 2.2e-175
phage_finder:164171330720 - 140018077CDS68 overlapping CDS - Eval: 1e-165
 
sherw:2692285976 - 233017255CDS
prophinder:355072286663 - 232417945CDS45 overlapping CDS - Eval: 5.9e-112
phage_finder:164212282874 - 234196068CDS55 overlapping CDS - Eval: 1e-133
 
sherw:2663551577 - 356570717CDS
prophinder:354853550280 - 355861013CDS9 overlapping CDS - Eval: 1.2e-19
 
sherw:2531849488 - 187926943CDS
prophinder:355121855818 - 187229025CDS25 overlapping CDS - Eval: 2.2e-60
phage_finder:164191866038 - 189320740CDS20 overlapping CDS - Eval: 4e-36
 
sherw:2501909139 - 193025022CDS
prophinder:355051887144 - 192763848CDS18 overlapping CDS - Eval: 2e-36
 
sherw:2641897625 - 190891115CDS
prophinder:355051887144 - 192763848CDS15 overlapping CDS - Eval: 1.2e-32
 
sherw:255300073 - 31025115CDS
prophinder:35467301940 - 30744610CDS10 overlapping CDS - Eval: 1.9e-26
phage_finder:16414300013 - 31064515CDS15 overlapping CDS - Eval: 4.2e-45
 
sherw:2652743223 - 278834851CDS
prophinder:355222746048 - 278834848CDS48 overlapping CDS - Eval: 3e-125
phage_finder:164232743224 - 278846150CDS50 overlapping CDS - Eval: 9.5e-134
 
sherw:2562118738 - 216569464CDS
prophinder:355212118738 - 216569464CDS64 overlapping CDS - Eval: 1.8e-166
phage_finder:164202115956 - 216579567CDS64 overlapping CDS - Eval: 3.1e-163
 
sherw:2622668339 - 268887029CDS
prophinder:354802678810 - 268837813CDS13 overlapping CDS - Eval: 4.8e-31
phage_finder:164222668052 - 271296655CDS29 overlapping CDS - Eval: 8.1e-68
 
sherw:2631879335 - 189762227CDS
prophinder:355051887144 - 192763848CDS15 overlapping CDS - Eval: 2.1e-25
phage_finder:164191866038 - 189320740CDS20 overlapping CDS - Eval: 3.8e-42
 
sherw:2571702185 - 172574831CDS
prophinder:355041709058 - 174421539CDS24 overlapping CDS - Eval: 1.1e-52
phage_finder:164181678525 - 176171099CDS31 overlapping CDS - Eval: 6.8e-63
 
sherw:2511250521 - 129545863CDS
prophinder:355011263856 - 129380242CDS42 overlapping CDS - Eval: 9.7e-99
phage_finder:164161250314 - 129562263CDS63 overlapping CDS - Eval: 1.2e-165
 
sherw:2581730065 - 175600630CDS
prophinder:355041709058 - 174421539CDS15 overlapping CDS - Eval: 4.3e-26
phage_finder:164181678525 - 176171099CDS30 overlapping CDS - Eval: 1.2e-60
 
sherw:2541626722 - 167348560CDS
prophinder:355311626722 - 166301552CDS52 overlapping CDS - Eval: 1.4e-129
 
Prophinder false negatives
sherw:2603263064 - 32704049CDS
 
Phage_Finder false negatives
sherw:252310756 - 32311217CDS
sherw:2663551577 - 356570717CDS
sherw:2603263064 - 32704049CDS
sherw:2501909139 - 193025022CDS
sherw:2541626722 - 167348560CDS
sherw:2641897625 - 190891115CDS
 
False positives
prophinder:355165387445 - 542442118CDS
 
NC_002758 Staphylococcus aureus subsp. aureus Mu50 - 2878529bp  Go to Prophinder
sherw:1742083515 - 212611062CDS
prophinder:356032083515 - 212445060CDS60 overlapping CDS - Eval: 3.8e-154
phage_finder:166192083115 - 212618162CDS62 overlapping CDS - Eval: 2.3e-163
 
sherw:173917507 - 96256571CDS
prophinder:35602919791 - 95943363CDS63 overlapping CDS - Eval: 3.5e-154
phage_finder:16618917414 - 96198370CDS70 overlapping CDS - Eval: 1.5e-179
 
False positives
prophinder:35596868462 - 8739359CDS
phage_finder:16617868335 - 88287122CDS
 
NC_004606 Streptococcus pyogenes SSI-1 - 1894275bp  Go to Prophinder
sherw:193545636 - 58360355CDS
prophinder:34755547834 - 58232448CDS48 overlapping CDS - Eval: 2.9e-121
phage_finder:16663545487 - 58369155CDS55 overlapping CDS - Eval: 3.2e-147
 
sherw:192625070 - 66633463CDS
prophinder:34769625070 - 66633463CDS63 overlapping CDS - Eval: 3.3e-164
phage_finder:16664624896 - 67572671CDS63 overlapping CDS - Eval: 1.3e-155
 
sherw:194446427 - 48616049CDS
prophinder:34754446427 - 48464547CDS47 overlapping CDS - Eval: 4e-124
phage_finder:16662446165 - 49531456CDS49 overlapping CDS - Eval: 1e-124
 
sherw:191725017 - 75914155CDS
prophinder:34733725017 - 73250815CDS15 overlapping CDS - Eval: 1.4e-31
prophinder:34760753223 - 7591418CDS8 overlapping CDS - Eval: 1.1e-14
prophinder:34738738922 - 75209919CDS19 overlapping CDS - Eval: 1.8e-41
phage_finder:16665724702 - 76450260CDS55 overlapping CDS - Eval: 1.7e-140
 
sherw:1901107957 - 114754355CDS
prophinder:347341133221 - 113889110CDS10 overlapping CDS - Eval: 1.8e-19
prophinder:347471139125 - 114603612CDS12 overlapping CDS - Eval: 2.7e-24
prophinder:347411110515 - 112724319CDS19 overlapping CDS - Eval: 1.8e-41
phage_finder:166671107624 - 115245758CDS55 overlapping CDS - Eval: 9.9e-143
 
sherw:195878690 - 91906461CDS
prophinder:34767878690 - 91906461CDS61 overlapping CDS - Eval: 1.1e-159
phage_finder:16666878343 - 92483965CDS61 overlapping CDS - Eval: 3e-155
 
NC_003919 Xanthomonas axonopodis pv. citri str. 306 - 5175554bp  Go to Prophinder
sherw:3273105263 - 311586815CDS
prophinder:325823104373 - 312078824CDS15 overlapping CDS - Eval: 1.5e-38
phage_finder:166793091075 - 312118138CDS15 overlapping CDS - Eval: 6.4e-35
 
sherw:3261211424 - 122867719CDS
prophinder:325771220880 - 124242719CDS10 overlapping CDS - Eval: 5.2e-20
phage_finder:166781209301 - 122908522CDS19 overlapping CDS - Eval: 2.9e-53
 
False positives
prophinder:325782197827 - 222598512CDS
 
Authors: Gipsi Lima Mendez, Ariane Toussaint and Raphael Leplae. Contact: Gipsi Lima Mendez