On Donnerstag 02 Juli 2009 Alexie Papanicolaou wrote: > > Can mira handle introns ? So for example if two parts of a read match > > well to a contig but are separated by a gap of more then 100 bps would > > mira handle this ? > > ehm... I really don't think MIRA would be the tool to use for what > essentially is a gapped alignment... A local alignment (with gaps) tool > such as BLAST, or better FASTA, would be necessary. You can then use % > identity to filter positives (two contigs from same locus) vs. negatives > (two contigs sharing the same protein domain)... MIRA will not be able to handle introns in a "mapping ESTs against a genome" scenario. Sorry. There are other specialised programs which do that. These you would feed with the EST consensus sequences MIRA builds. Regards, Bastien -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html