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Old 10-27-2012, 08:38 AM   #1
lee27
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Location: Ithaca, NY

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Default Transcriptome to transcriptome alignment

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
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Old 10-27-2012, 08:43 AM   #2
Richard Finney
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Check out blat from Jim Kent at UCSC or blast from NCBI.
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Old 10-27-2012, 10:00 AM   #3
figo1019
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Quote:
Originally Posted by lee27 View Post
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 .
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Old 10-28-2012, 09:13 AM   #4
JackieBadger
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http://www.plosone.org/article/info%...l.pone.0007767
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