how to find exon combination of a given transcript

[TPH]

Hi,

I have a set of transcript sequences retrieved from cufflinks output through gffread -w and a pool of exon sequences of the gene of interest. Transcripts have unique ids given by cufflinks (eg: CUFF.11523.1). I want to know which exons are present and absent in each of them.
The only method come to my mind is doing a pairwise alignment between each exon and transcript. Since the gene of interest has more than 300 exons, that would be so time consuming.
Is there any other method or software out there which could be used to obtain exon composition or is pairwise alignment is the only solution?

Really appreciate any comment or suggestion on this.

Thank you very much

TPH

[Melissa]

It's always a problem getting primary transcript without genome annotation. I'll probably use bedtools merge to merge all the transcripts into one long transcript and then use bedtools intersect to check which transcript contains which exons. You need to play with the coordinates not sequences.

[TPH]

Hi Melissa,
Thank you for the reply. Will give a try on Bedtools then.
Best,
Pabodha