In article <bcor4j$ok4$1 at charm.magnus.acs.ohio-state.edu>, Vayuputra wrote:
> Is there an online resource which allows me to align a cDNA sequence with a
> corresponding genomic sequence? In other words, if I'm trying to find out
> the intron-exon structure of a cDNA I have with some genomic sequence
> information I obtained, what's the best way to get the intron-exon structure
> info.?
I believe that BLAT is now the preferred tool for such alignments. If
your sequence is human, mouse, rat, or SARS, go to genome.ucsc.edu and
click on the BLAT page (other genomes to come sometime this summer, I
believe).
http://www.soe.ucsc.edu/~kent/src/
has the source code for BLAT if you need it.
--
Kevin Karplus karplus at soe.ucsc.eduhttp://www.soe.ucsc.edu/~karplus
Professor of Computer Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
Affiliations for identification only.
