Beefy Boxes and Bandwidth Generously Provided by pair Networks
There's more than one way to do things

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]
[marto]: Corion worse, some plant inspection, cameras moving thru pipes
[marto]: Discipulus yeah, just don't adopt his tactics :P
[marto]: the content for the most part is fairly dull, but if they go for it, they can use it for all sorts of video, they have no solution for this at the moment
[Discipulus]: with "thru pipes" you mean bot cameras moving inside pipes?!?

How do I use this? | Other CB clients
Other Users?
Others pondering the Monastery: (8)
As of 2017-07-28 09:29 GMT
Find Nodes?
    Voting Booth?
    I came, I saw, I ...

    Results (425 votes). Check out past polls.