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linsalrob / PhiSpy

Prediction of prophages from bacterial genomes
MIT License
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some problem with position of att site and prophage region #59

Open work-liuyang opened 2 years ago

work-liuyang commented 2 years ago

The sequences of att site and prophage region in the output files decrease a base comparing with the sequences we extracted by positions in outfiles.So,which is the correct result?Thank you.

linsalrob commented 2 years ago

Can you please provide an example of the genome and output, and what should happen? This sounds like an off-by-one error that we missed.

Rob

work-liuyang commented 2 years ago

problem.pdf I forgot to reply to you.I'm so sorry . I wrote the detailed explanation in a pdf file.Thank you very much for your help!

If it's not convenient for you to download the file,the description of PDF file is: as shown in the figure，this is an output file by using PhisPy(4.2.19).the start position and end position of attL are 1868451 and 1868465,then the sequence is “AATTATCATTATTT”.However,I used seqkit tools(seqkit subseq -r 1868451:1868465 genome.fa) to extract sequence from start position and end position,the sequence is “AATTATCATTATTTA” .Obviously,the result I extracted have an extra base(“A”) at the end,comparing to the sequence of output.That is to say,the description of postion and sequence is not matched.By the way,the positon of prophage also doesn’t match with sequence in “phage.fasta” generating by PhiSpy.Which result should I choose?By position or sequence?

linsalrob commented 2 years ago

seqkit subseq is taking the sequence from 1868451 to 1868465 including the base at position 1868465. We are (probably incorrectly) reporting the repeat to go from 1868451 to 1868465 not including the base at position 1868465. The repeat AATTATCATTATTT is 14 bases so we should end it at 1868464.

I will check this off by one error and correct it.

work-liuyang commented 2 years ago

I got it，that is to say，the phage sequence I extracted from position have an extra base at the start comparing to the output by PhiSpy，so the true start position of phage should be 1866818 rather than 1866817。