Beefy Boxes and Bandwidth Generously Provided by pair Networks
Keep It Simple, Stupid
 
PerlMonks  

inexact PAttern searching

by Chauds09 (Initiate)
on Mar 10, 2012 at 16:33 UTC ( #958875=perlquestion: print w/ replies, xml ) Need Help??
Chauds09 has asked for the wisdom of the Perl Monks concerning the following question:

I have a Multi sequence FASTA file with headers followed by the respective DNA sequences. I need to split the file into separate sequences and done in such a way that i can do some pattern searching within each individual sequence, by printing out the location of the pattern within the sequence. Can some one help me out regarding this matter?

Comment on inexact PAttern searching
Re: inexact PAttern searching
by bitingduck (Friar) on Mar 10, 2012 at 17:02 UTC

    It sounds like something that should be straightforward, but probably nobody here knows what a FASTA file is. If you can post a sample of the input and a sample of the expected output, that would help a lot. Posting some code that you've started with would help even more-- there have been a bunch of bioinformatics problems with responses posted over the past few days that you could probably use as a starting point

      A professor somewhere directed all students towards Perlmonks...:)
Re: inexact PAttern searching
by erix (Vicar) on Mar 10, 2012 at 17:10 UTC

    If you search this site there is already a good chance that you will be able to help yourself.

    Just type 'fasta' into the search input on the upper left corner of each page, or use the 'Super Search' page: Super Search.

Re: inexact PAttern searching
by tangent (Deacon) on Mar 10, 2012 at 17:55 UTC
    Have a look at this node - I think it deals with the same type of file
Re: inexact PAttern searching
by TJPride (Pilgrim) on Mar 11, 2012 at 06:38 UTC
    Paste a sample of your file, and a sample of the desired output.

Log In?
Username:
Password:

What's my password?
Create A New User
Node Status?
node history
Node Type: perlquestion [id://958875]
Approved by Limbic~Region
help
Chatterbox?
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others musing on the Monastery: (9)
As of 2014-10-21 21:54 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?

    For retirement, I am banking on:










    Results (111 votes), past polls