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linsalrob / ProphagePredictionComparisons

Comparisons of multiple different prophage predictions
MIT License
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Missing prophage in Escherichia coli K12 #8

Open apcamargo opened 3 years ago

apcamargo commented 3 years ago

Hey Rob!

The Escherichia coli K12 genome seems to be missing more than one prophage. Here's one that I curated manually:

contig       gene                            start      end
---------------------------------------------------------------
NC_000913    RAST2:fig|83333.998.peg.2428    2464528    2465722
NC_000913    RAST2:fig|83333.998.peg.2429    2466233    2467154
NC_000913    RAST2:fig|83333.998.peg.2430    2467150    2468482
NC_000913    RAST2:fig|83333.998.peg.2431    2468822    2469125
NC_000913    RAST2:fig|83333.998.peg.2432    2469096    2469537
NC_000913    RAST2:fig|83333.998.peg.2433    2469563    2470157
NC_000913    RAST2:fig|83333.998.peg.2434    2470131    2470407
NC_000913    RAST2:fig|83333.998.peg.2435    2470406    2470901
NC_000913    RAST2:fig|83333.998.peg.2436    2470897    2471266
NC_000913    RAST2:fig|83333.998.peg.2437    2471415    2471589
NC_000913    RAST2:fig|83333.998.peg.2438    2471623    2471986
NC_000913    RAST2:fig|83333.998.peg.2439    2472051    2472876
NC_000913    RAST2:fig|83333.998.peg.2440    2473003    2473540
NC_000913    RAST2:fig|83333.998.peg.2441    2473530    2473893
NC_000913    RAST2:fig|83333.998.peg.2442    2473892    2474198
NC_000913    RAST2:fig|83333.998.peg.2443    2474329    2474530

There's also a clear prophage that starts with RAST2:fig|83333.998.peg.1592, but I couldn't determine its other boundary.