search

xiezhq / ISEScan

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
Apache License 2.0
79 stars 17 forks source link

Question about Results #18

Closed lancetxiao closed 4 years ago

lancetxiao commented 4 years ago

Dear Xie, Thanks for this great IS tools. However, I don't understand the %Genome in the sum results. Because I can not figure out the "dnaLen: length of the specific sequence". What is the "specific sequence"？

xiezhq commented 4 years ago

Hi lancetxiao,

ISEScan treats each sequence in a fasta file as an independent genome sequence (DNA sequence). So, the 'specific sequence' is one DNA sequence, namely, a sequence following a head line starting with '>' in your input fasta file (e.g. the sequence with seqid 'gi|228288719|ref|NC_012624.1|' in NC_012624.fna). It will be clear if you can try running ISEScan on a fasta file containing multiple sequences and have a look at the output file *.sum file.

Xie