Module

Discussion in 'Perl Misc' started by Rita, Nov 16, 2005.

  1. Rita

    Rita Guest

    i have 2 sequences like
    ASDFGHJKLOIUYTREWQ and
    ASDHJKLTREWQ

    so when we align both sequence there is some GAP like
    FG
    OIUY.
    so is there some module which can find this type of gap sequences.
    thanks
     
    Rita, Nov 16, 2005
    #1
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  2. Rita

    Guest

    Rita wrote:
    > i have 2 sequences like
    > ASDFGHJKLOIUYTREWQ and
    > ASDHJKLTREWQ


    In your example data, the second sequence comprises a subset of the
    first. Will this always be the case? Or could you have sequences like
    this:

    ASDFGHJKLOIUYTREWQ
    ASabcDHJKLTREWQ

    where the second sequence has elements not found in the first?
     
    , Nov 16, 2005
    #2
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  3. Rita

    Rita Guest


    > In your example data, the second sequence comprises a subset of the
    > first. Will this always be the case? Or could you have sequences like
    > this:
    >
    > ASDFGHJKLOIUYTREWQ
    > ASabcDHJKLTREWQ
    >
    > where the second sequence has elements not found in the first?

    no. second one is always subsequence of first one
     
    Rita, Nov 16, 2005
    #3
  4. Rita

    Eden Cardim Guest

    Rita escreveu:

    > i have 2 sequences like
    > ASDFGHJKLOIUYTREWQ and
    > ASDHJKLTREWQ
    >
    > so when we align both sequence there is some GAP like
    > FG
    > OIUY.
    > so is there some module which can find this type of gap sequences.
    > thanks


    I can tell from your posts that you're into bioinformatics. The tool
    you're looking for is called BLAST (Basic Local Alignment and Search
    Tool) and can be found at NCBI (http://www.ncbi.nlm.nih.gov/BLAST/).
    The Bioperl project (www.bioperl.org) provides modules with several
    bioinformatics tools, including a front-end for BLAST. You can get all
    the latest bioperl modules from CPAN.
     
    Eden Cardim, Nov 16, 2005
    #4
  5. Rita

    Rita Guest

    Eden Cardim wrote:
    > Rita escreveu:
    >
    > > i have 2 sequences like
    > > ASDFGHJKLOIUYTREWQ and
    > > ASDHJKLTREWQ
    > >
    > > so when we align both sequence there is some GAP like
    > > FG
    > > OIUY.
    > > so is there some module which can find this type of gap sequences.
    > > thanks

    >
    > I can tell from your posts that you're into bioinformatics. The tool
    > you're looking for is called BLAST (Basic Local Alignment and Search
    > Tool) and can be found at NCBI (http://www.ncbi.nlm.nih.gov/BLAST/).
    > The Bioperl project (www.bioperl.org) provides modules with several
    > bioinformatics tools, including a front-end for BLAST. You can get all
    > the latest bioperl modules from CPAN.

    thanks,i know about BLAST but after BLAST i want the sequence whis is
    not aligning so is there any module for that.
     
    Rita, Nov 16, 2005
    #5
  6. Rita

    Eden Cardim Guest

    > thanks,i know about BLAST but after BLAST i want the sequence whis is
    > not aligning so is there any module for that.


    Oh, now I understand what you want, the solution is simple so I don't
    think anyone would have coded a specific module for that, maybe you can
    find a toolkit at CPAN. Here's a way to get at the gaps in the
    sequences:

    ($gap) = $sequence =~ /$match1(.+?)$match2/;
     
    Eden Cardim, Nov 16, 2005
    #6
  7. Rita

    Rita Guest


    > Oh, now I understand what you want, the solution is simple so I don't
    > think anyone would have coded a specific module for that, maybe you


    Thank you so much for your help! I couldn't figure it out.
     
    Rita, Nov 17, 2005
    #7
  8. Rita

    Rita Guest

    Eden Cardim wrote:
    > > thanks,i know about BLAST but after BLAST i want the sequence whis is
    > > not aligning so is there any module for that.

    >
    > Oh, now I understand what you want, the solution is simple so I don't
    > think anyone would have coded a specific module for that,

    It looks like you Know about Bioinformatics.i started to do it and i
    red the book that Beginning Perl for Bioinformatics.but i think ,i
    should read some more books or online documents about it so can you
    sggest me some name .

    > ($gap) = $sequence =~ /$match1(.+?)$match2/;

    what will be value of $sequence and $match1 ,$match2.
    and if i have more than 1 gap in my sequence then is it find that too
    or i have to put in a loop or something.
    thanks
     
    Rita, Nov 17, 2005
    #8
  9. Rita

    Eden Cardim Guest

    > It looks like you Know about Bioinformatics.i started to do it and i
    > red the book that Beginning Perl for Bioinformatics.but i think ,i
    > should read some more books or online documents about it so can you
    > sggest me some name .


    amazon.com
    search for books with "perl bioinformatics"

    > > ($gap) = $sequence =~ /$match1(.+?)$match2/;

    > what will be value of $sequence and $match1 ,$match2.


    an example with the data you provided previously:

    $sequence = "ASDFGHJKLOIUYTREWQ";
    $match1 = "ASD";
    $match2 = "HJKL";
    ($gap) = $sequence =~ /$match1(.+?)$match2/;
    #$gap now contains "FG";

    > and if i have more than 1 gap in my sequence then is it find that too
    > or i have to put in a loop or something.
    > thanks


    yes, you need a loop, I haven't dealt directly with BLAST output for a
    long time now so I'm not sure how it represents alignment gaps, I think
    it uses '-', so you would need to split on that.
    I suggest you do some more reading about Perl before actually building
    production code.
     
    Eden Cardim, Nov 17, 2005
    #9
  10. Rita

    Rita Guest

    Eden Cardim wrote:
    > > It looks like you Know about Bioinformatics.i started to do it and i
    > > red the book that Beginning Perl for Bioinformatics.but i think ,i
    > > should read some more books or online documents about it so can you
    > > sggest me some name .

    >
    > amazon.com
    > search for books with "perl bioinformatics"
    >
    > > > ($gap) = $sequence =~ /$match1(.+?)$match2/;

    > > what will be value of $sequence and $match1 ,$match2.

    >
    > an example with the data you provided previously:
    >
    > $sequence = "ASDFGHJKLOIUYTREWQ";
    > $match1 = "ASD";
    > $match2 = "HJKL";
    > ($gap) = $sequence =~ /$match1(.+?)$match2/;
    > #$gap now contains "FG";
    >
    > > and if i have more than 1 gap in my sequence then is it find that too
    > > or i have to put in a loop or something.
    > > thanks

    >
    > yes, you need a loop, I haven't dealt directly with BLAST output for a
    > long time now so I'm not sure how it represents alignment gaps, I think
    > it uses '-', so you would need to split on that.
    > I suggest you do some more reading about Perl before actually building
    > production code.

    thanks
     
    Rita, Nov 17, 2005
    #10
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