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Aligning RNA to genomic DNA

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Aligning RNA to genomic DNA

Postby simplitia » Wed Sep 25, 2013 6:53 pm

Hi all,
does anyone have a recommendation for gap open penalty and extension penalty setting - what I'm trying to do is to align an RNA seqeunce which is compose of exon 1 and 2 to a genomic DNA - however so far it I can only align either exon 1 or 2 but not both because there is a huge intronic gap in the gDNA. I tried reducing the gap open penalty to about 2 and increase extension to 20 but still does not work. I used several programs already including clustal and genieous but so far no go. Thanks in advance.
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Postby JackBean » Fri Sep 27, 2013 8:17 am

In contrary you need to increase the open penalty and decrease the extension penalty, so that it will favour long uninterupted gaps instead of many small gaps.

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