BLAST for spliced isoforms?

[tboothby]

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.

[rskr]

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

[tboothby]

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

[rskr]

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

[tboothby]

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?

[rskr]

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.

[tboothby]

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

[rskr]

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.

[tboothby]

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