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  • to decide whether a mutation is non-synonimous or not

    i have short solexa sequences mapping to genome, in some positions there're
    some certain enriched mutations, how do i know whether this mutation is non-synonimous or not ?
    one method is download transcript isoforms and coding annotations from ucsc, then count from the coding start site to determine what codon this position belong to then go to codon - Aa table t ocheck, can anyone give me better method ? thanks in advance

    also, i have checked, in biomart we can download phase information ~
    maybe i will use this

    ZSL
    Last edited by zslee; 12-07-2009, 11:57 PM.

  • #2
    Is this human genomic? If it is, we have been using SIFT for this with great success.

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    • #3
      Originally posted by brasj View Post
      Is this human genomic? If it is, we have been using SIFT for this with great success.
      SIFT (Sorting Intolerant From Tolerant) is a program that predicts whether an amino acid substitution affects protein function
      my work is simpler, i just want to know whether a change of bases on human genome affect the amino acide coded, maybe SIFT can be used next step of my project,
      so thanks a lot ~~

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      • #4
        Your original proposal is pretty much the definition of how to do it; under what metric is it less than ideal?

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        • #5
          I would think BLASTx is the tool of choice here. You determine where in your sequence your change is, and make sure that the BLASTx match covers that letter.

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          • #6
            No, BLASTX is very poor choice for multiple reasons:

            1) Misclassifications, both false positive & false negative, around splice junctions
            2) Speed. Much slower than doing lookup.
            3) Very short exons will be missed
            4) More risk of confusing paralogs & pseudogenes with your actual gene

            Mapping the position to annotated transcript(s) and then computing the new codon & comparing its translation to the old codon is fast, simple & guaranteed. Hard to see why one would choose slow & error-prone over that.

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            • #7
              guys, give sift a look.

              you stick all your variants in there and it outputs a list of all of them that are coding and the change it does in the protein. Additionally, it also gives them a score of "tolerability".

              if I understood correctly, this does all you need... and more

              Assuming this is human dna, of course.

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              • #8
                thanks to you all
                i 'll first use krobison's suggestion and consider sift later
                ~~

                Comment


                • #9
                  There is another thread on this topic -

                  Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


                  Myself and some others have already developed scripts for this.
                  Sift is good, but is for the human genome only.

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