Fast Pairwise Alignments Of Assembled Transcripts

Question

[James Smith]

I've done a transcriptome assembly and need to now determine if my results are worth while to pursue. I have a reference of cdna from this same organism that I want to compare these assembled transcripts to. Is there a recommended aligner or software for this? I'm looking at Exonerate right now. However I've been recommended Blat, which, I don't think is appropriate for this task.

[Travis]

Do you not have a reference genome?

Answer 1

[2184687-1231-83-]

I think exonerate is a good choice, since it will allow you to assess if your transcript contigs are in frame to translate for proteins, using --model cdna2genome. Also, if you believe you may have frameshifts in your transcript contigs, you can still get proper alignments with the --frameshift parameter.

Answer 2

[Vitis]

I sort of have faced the same task but I used BLAT. It was quite fast and the output was easy to parse. I don't know the exact reason why you don't think it's appropriate, maybe you can elaborate?

[Vitis]

Yes, BLAT was best for mapping cDNA or ESTs to the genome as it seems to be optimized for that kind of tasks. But I think it would do just fine because your reference transcripts are high quality.

[James Smith]

The Blat documentation states that it's used for aligning sequences to genomes. Since it's not designed for transcript sized reads, I'm afraid that it's not going to be sensitive enough for shorter sequences. However, upon further investigation, it seems like many people have used blat (and published) with no problem.