<p>I've assembled a de novo transcriptome from RNAseq data. I'm comparing it against a reference cDNA set that is publicly available. However, I'd like to see if my assembly has produced any novel transcripts. Is there something like a reverse alignment? I'd like to find transcripts that I've assembled that are not included in this file of cDNA. I will then map them to the genome using blat or a similar tool.</p>

<p>How can I do what seems like the inverse of an alignment?</p>

Check here : 

https://www.biostars.org/p/14863/
