[mira_talk] Re: mira and introns

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


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