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  • BLAST for spliced isoforms?

    Hey,
    Does anyone know if it is possible to setup a stand alone BLAST search that will return spliced isoforms?

    I was thinking something that would look for alignments followed by a break of some minimum size (say 50bp) followed by more alignments...

    Is there a better way to do this? I have RNAseq data but no reference genome. I am looking for a way to find all the spliced isoforms in this data.

    Thanks.

  • #2
    Assemble your data first then map the assemblies, that is my recommendation.

    Comment


    • #3
      I have assembled sequences... so then I map the rnaseq sequences to themselves? What software?

      Comment


      • #4
        Map the contigs with BLAST or whatever rna, est mapping software you want.

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        • #5
          right... I am asking if there is a way to setup a stand alone BLAST search to specifically return only likely splice isoforms. Do you know how to do this?

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          • #6
            BLAST? I think there is a set of tools at NCBI called splign and spidey that will chain together HSPs with a Gene model. BLAST is kind of a dum way to do it IMO, but lots of people have used BLAST for things it wasn't designed for before in the past.

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            • #7
              Yea, but don't you use a genomic reference for those? No reference genome here unfortunately.

              Comment


              • #8
                Ah yes, mapping mRNA to mRNA with exons. I don't know a way to do that, but I was wishing BLAST would do that just yesterday.

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                • #9
                  Ah well, if you don't know how to do it then maybe someone else does.

                  Comment

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