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  • Program to relate SNPs to model genome annotation?

    EMS-mutagenesis causes G->A and C->T transitions. In most cases large numbers of these lesions are produced per genome with only one being the source of mutant phenotype screened for.

    I have a lists of 50-100 of these mutations/genome for a number of yeast strains as determined from a SOLiD sequencing run.

    What is the recommended method to convert this information (single base change at a known genomic location) to gene name and effect on the gene (eg, synonymous--no change to protein sequence, 1 residue change to sequence, or truncation)? Seems like something that would already have been written.

    --
    Phillip
    Last edited by pmiguel; 04-13-2010, 07:29 AM. Reason: Typo

  • #2
    Originally posted by pmiguel View Post
    What is the recommended method to convert this information (single base change at a known genomic location) to gene name and effect on the gene (eg, synonymous--no change to protein sequence, 1 residue change to sequence, or truncation)? Seems like something that would already have been written.
    The "consequences" module in our software Nesoni (*) does this... BUT it requires you to use the previous "shrimp" (align) and "consensus" (call) modules beforehand - all the modules share a folder of results. It is mainly useful for bacterial genomes, so perhaps not as useful to you.

    If it is only subsitutions and not indels, it's a pretty simple BioPerl script to take your list and a Genbank file of the genome and test the effects on each CDS.

    (*) Nesoni http://www.vicbioinformatics.com/software.nesoni.shtml

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    • #3
      Originally posted by Torst View Post
      The "consequences" module in our software Nesoni (*) does this... BUT it requires you to use the previous "shrimp" (align) and "consensus" (call) modules beforehand - all the modules share a folder of results. It is mainly useful for bacterial genomes, so perhaps not as useful to you.

      If it is only subsitutions and not indels, it's a pretty simple BioPerl script to take your list and a Genbank file of the genome and test the effects on each CDS.

      (*) Nesoni http://www.vicbioinformatics.com/software.nesoni.shtml
      Does it handle multiple exon genes okay? I notice you are primarily a bacterial informatics shop...

      Thanks for the response,
      Phillip

      Comment


      • #4
        Originally posted by pmiguel View Post
        Does it handle multiple exon genes okay? I notice you are primarily a bacterial informatics shop...
        Yes as I said we are bacteria focussed. Even in bacteria we have introns sometimes, and pseudo genes are often written as join(a..b,c..d) for the N-term and C-term "exons". Nesoni uses BioPython for the annotation retrieval, so it *may* work. I will talk to the primary author and find out; it probably isn't difficult to alter to work with join() features. You could try it on a small chromosome? (Assuming you have a server with enough RAM)

        --Torst

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        • #5
          Originally posted by Torst View Post
          Yes as I said we are bacteria focussed. Even in bacteria we have introns sometimes, and pseudo genes are often written as join(a..b,c..d) for the N-term and C-term "exons". Nesoni uses BioPython for the annotation retrieval, so it *may* work. I will talk to the primary author and find out; it probably isn't difficult to alter to work with join() features. You could try it on a small chromosome? (Assuming you have a server with enough RAM)

          --Torst
          Hi Torst,
          Thanks again for you response. I ended up writing a script employing bioperl to do this. Initially I thought it would take me less time than acquiring and installing Nesoni. But since it took me several days to write and debug my code I was probably wrong.
          Phillip

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