Beefy Boxes and Bandwidth Generously Provided by pair Networks
We don't bite newbies here... much

Re: parsing mismatch from blast output

by BioLion (Curate)
on Aug 09, 2010 at 14:56 UTC ( #853841=note: print w/replies, xml ) Need Help??

in reply to parsing mismatch from blast output

Boulder::Blast is probably one standard way of parsing BLASTN results (and other tag/val reports), and will do a good job of simplifying the data held in the record, from where you could split the match and reference sequences into individual characters, and compare them, outputting mismatched characters (and their positions within the match).

You might also want to check out bioperl: parse BLAST HSPs which gives some example code on handling the records, to get at the info you want.

Hope this helps - have a go, and if you get into further trouble re-post and I am sure many a Monk will rush to your aid - remember to include input/code/outpur/error messages etc...!

Just a something something...

Log In?

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://853841]
and all is quiet...

How do I use this? | Other CB clients
Other Users?
Others imbibing at the Monastery: (4)
As of 2018-07-21 08:11 GMT
Find Nodes?
    Voting Booth?
    It has been suggested to rename Perl 6 in order to boost its marketing potential. Which name would you prefer?

    Results (445 votes). Check out past polls.