Hi,
I would like to filter my blastn output to look at hits in their full length relative to the query, not just including the matching part.
One way, I came up with, is to filter all output to have the same length (or longer) as the query sequence.
Alternatively it would help me very much, if there was a way to calculate the perc_identity relative to to the whole length of the query and not to just to the match.
Is there a way, that I can play with word_size to allow mismatches? Then I could just set the word_size to the query length...
(in my case, just mismatches are important, I would not allow for insertions or deletions anyway)
Does anybody have an idea, how I could solve this, or how I can practically implement the ideas that I had?
Thank you very much!
I would like to filter my blastn output to look at hits in their full length relative to the query, not just including the matching part.
One way, I came up with, is to filter all output to have the same length (or longer) as the query sequence.
Alternatively it would help me very much, if there was a way to calculate the perc_identity relative to to the whole length of the query and not to just to the match.
Is there a way, that I can play with word_size to allow mismatches? Then I could just set the word_size to the query length...
(in my case, just mismatches are important, I would not allow for insertions or deletions anyway)
Does anybody have an idea, how I could solve this, or how I can practically implement the ideas that I had?
Thank you very much!
Comment