In article <l03130300b47583fa4af0@[132.183.189.39]>,
bongard at FRODO.MGH.HARVARD.EDU ("Deverie K. Bongard-Pierce") wrote:
> Version 3 of Sequencher does not do as well as the Phred/Phrap/Consed trio
> when it comes to aligning EST sequences with their genomic counterparts-
> alot more editing is need around intron borders, but again I have heard
> that the ver.4 software does a much better job with these kinds of
> alignments.
If you want to align ESTs and cDNA sequences to genomic DNA you should try
est2genome
http://www.sanger.ac.uk/Software/EMBOSS/Apps/est2genome.shtml
