Mapping cDNA's to assembly

[k-gun12]

I've got a partial assembly of a low coverage genome (about 250k contigs) and a set of assembled cDNAs I'd like to map to those contigs to get a first guess as to where the introns lie, etc-. Is there a nice piece of software that'll do that relatively quickly? I suppose I could do it with several rounds of blast, or even script a pipeline that makes a blast DB from each assembled genome contig and runs the cnda against it, but I figured I'd ask here first. Visualization would also be a nice plus...

Thanks!

[tcezard]

Blast would be an option and you can then use the script blast2sam.pl from samtools to get the sam version and vizualise with IGV

[Zigster]

I find BLAT has a better understanding of spliced alignments

I use Don Gilbert's blat2gff.pl and view in gbrowse

http://iubio.bio.indiana.edu/gmod/tandy/blat2gff.pl

[tcezard]

Don't know if it's relevent but I just read the BWA for long read paper. you could have a look at that

http://bioinformatics.oxfordjournals.org/cgi/content/short/26/5/589?rss=1

[dcjamison]

mgalign also has a much better understanding of spliced alignments than BLAST.

http://proline.bic.nus.edu.sg/mgalign/mgalignit.html

I used this to annotate a velvet assembly and was quite pleased at the results. The output is easily translated to genepred or bed formats.