Beefy Boxes and Bandwidth Generously Provided by pair Networks
Do you know where your variables are?
 
PerlMonks  

Re: Re: Re: BioInformatics - polyA tail search

by Anonymous Monk
on Sep 03, 2003 at 12:18 UTC ( [id://288603]=note: print w/replies, xml ) Need Help??


in reply to Re: Re: BioInformatics - polyA tail search
in thread BioInformatics - polyA tail search

Are you sure that's what you want? You know your problem-space, so I'm just checking. There are three issues I see:

  1. Fasta doesn't have to be 80 characters per-line
  2. Fasta doesn't have to be ctrl-M delimited
  3. Are you sure you don't want to check strand identity (e.g. look for poly-T sequences)?

Either way, the simple answer is to parse the file using SeqIO (BioPerl). Extract the sequence, then run a reg-ex to look for what you want. In your case it's $seq =~ /[AN]{10,}/ I think.

Log In?
Username:
Password:

What's my password?
Create A New User
Domain Nodelet?
Node Status?
node history
Node Type: note [id://288603]
help
Chatterbox?
and the web crawler heard nothing...

How do I use this?Last hourOther CB clients
Other Users?
Others avoiding work at the Monastery: (4)
As of 2024-03-28 22:40 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?

    No recent polls found