[mira_talk] Re: mira and introns
- From: Alexie Papanicolaou <alpapan@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 02 Jul 2009 10:39:26 +0100
Hello
> 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)...
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