transcriptome aligment insteat of genome

[nicedad]

Usually people align their transcriptome or genome to a genome reference.

My question is, is it possible to aligne transcriptome of a non-model species to another transcriptome of a closely related species instead of genome?

shouldn't this be much easier than aligning with the entire genome? although I've not seen anyone did this!

any input will be appreciated,

[rskr]

There aren't many suitable aligners for transcript databases. Even in the blast suite it is either dna to dna or rna to dna but not rna to rna, and there are some definite differences including codons, stop codons, and splicing. I think most people just create dna databases, and do dna alignments. I am interested in finding out if there is a good rna to rna aligner available.

[nicedad]

rskr...thanks for the replay,
I aligned cDNA of a non-model insect of my interest to a closely related insect using 454aligner I got genes overlapping and SNPsand. Everything went perfectly however am not sure whether this is a good approach.

any suggestions?

[gringer]

In trying to get a better transcriptome for the same species, I used minimus2:

http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus2

The combined assembly is stored in an AMOS database, which can be queried to find overlaps and singleton sequences. I found this useful for mapping a novel transcriptome to one that was already known.

[rskr]

In trying to get a better transcriptome for the same species, I used minimus2:

http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus2

The combined assembly is stored in an AMOS database, which can be queried to find overlaps and singleton sequences. I found this useful for mapping a novel transcriptome to one that was already known.

Does minimus2 work with thousands of sequences? It seems to be based on nucmer, and last I checked it had problems with thousands of sequences, like a number programs in the AMOS package, not to mention primarily being designed for working with DNA.

[gringer]

It worked for me with thousands of sequences vs thousands of sequences, but only for transcriptomes (i.e. not the rather messy genomic reference sequence that I have for S. mediterranea).

[nicedad]

Thanks a lot everyone.
best,