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Old 09-07-2011, 06:21 AM   #1
tboothby
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Default 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.
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Old 09-07-2011, 07:16 AM   #2
rskr
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Assemble your data first then map the assemblies, that is my recommendation.
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Old 09-07-2011, 07:28 AM   #3
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I have assembled sequences... so then I map the rnaseq sequences to themselves? What software?
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Old 09-07-2011, 07:37 AM   #4
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Map the contigs with BLAST or whatever rna, est mapping software you want.
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Old 09-07-2011, 07:39 AM   #5
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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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Old 09-07-2011, 07:44 AM   #6
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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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Old 09-07-2011, 07:57 AM   #7
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Yea, but don't you use a genomic reference for those? No reference genome here unfortunately.
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Old 09-07-2011, 08:10 AM   #8
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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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Old 09-07-2011, 08:20 AM   #9
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Ah well, if you don't know how to do it then maybe someone else does.
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