Transcriptome to transcriptome alignment

[lee27]

Hello!
I have assembled a de novo transcriptome and would like to align my transcriptome (as assembled) to an existing transcriptome of a related species. The software I am familiar with only aligns reads to assemblies. Recommendations on software able to do this alignment? Thank you!
Cheers, Laura

[Richard Finney]

Check out blat from Jim Kent at UCSC or blast from NCBI.

[figo1019]

Hello!
I have assembled a de novo transcriptome and would like to align my transcriptome (as assembled) to an existing transcriptome of a related species. The software I am familiar with only aligns reads to assemblies. Recommendations on software able to do this alignment? Thank you!
Cheers, Laura

Hi , I am trying with the BLASTX with the Amino acids of the reference genome. Another way also can be try BLAT with the Transcriptome and take out the best hits and make the alignment. Some one suggested the Reciprocal BLAST also to be sure .

[JackieBadger]

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0007767