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linsalrob / PhiSpy

Prediction of prophages from bacterial genomes
MIT License
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Coordinates interpretation #56

Closed iferres closed 2 years ago

iferres commented 2 years ago

Hi, I have a question. Not a specialist on prophages but my understanding was that the attL/attR sequences were always flanking the prophage regions. I got the following prophage_coordinates.tsv file:

pp1             NODE_3  400     2596    1645    1657    3009    3021    GTCATAAAAGCC    GGCTTTTATGAC    Longest Repeat flanking phage and within 2000 bp
pp2             NODE_13 180     8557    3204    3216    7661    7673    TCGTCCAATTTC    GAAATTGGACGA    Longest Repeat flanking phage and within 2000 bp
pp3             NODE_14 15647   28479   14471   14484   25382   25395   AGGGAGTTTTACC   GGTAAAACTCCCT   Longest Repeat flanking phage and within 2000 bp
pp4             NODE_47 10784   27254   11925   11937   23917   23929   TGAATCGCAGTA    GCTAACCAAAGA    Longest Repeat flanking phage and within 2000 bp
...

As you can see, the prophage coordinates look weird with respect to the attL/attL's. I'm not sure if I am missing something or if there's a bug in PhiSpy. Am I interpreting the results the wrong way? Thanks!

iferres commented 2 years ago

Conda was installing an old version, failed with latest (4.2.21). May be that's the problem. Closing, I will open it again if the problem persist.