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Re: Re: Re: Re: BioInformatics - polyA tail search

by MiamiGenome (Sexton)
on Sep 02, 2003 at 18:36 UTC ( #288380=note: print w/replies, xml ) Need Help??

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

You are correct, but when the automated sequencers can not unambiguously choose the A,C,T,or G, they assign 'N'.

My chosen example sequences were from the beginning of a sequence file. PolyA stretches are found at the end.

Cheers, and thank you in advance!

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Re: Re: Re: Re: Re: BioInformatics - polyA tail search
by BrowserUk (Patriarch) on Sep 02, 2003 at 19:14 UTC

    Something like this will get you started.

    perl -nle" print "$ARGV:($./$+[0]): $1" if m[([AN]{10,}]g;" file*

    This will print lines like

    filename:(10/50): ANNNANANAAN

    where the first number is theline in the file and the second is the offset within the line.

    For unix you need to swap "s for 's, and under Win32 you would need to add BEGIN{ @ARGV=map{ glob } @ARGV } to expand the wildcard filespec supplied on the comand line.

    See perlrun for the switches used, and perlre for the regex.

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