[maker-devel] Short introns

[Shaun Jackman]

Hi, Carson.

I’m using protein evidence and protein2genome alone without ab initio gene finders to annotate an organellar genome. MAKER annotates 16 introns. 6 introns look real (according to RNAweasel) and are all larger than 900 bp. The other 10 introns are all shorter than 250 bp and multiples of 3 bp. These short introns look like genomic insertions rather than introns to me. Is there a way to specify a minimum intron size to MAKER?

6 of these short introns do not contain a stop codon, and 4 do contain a stop codon. I suppose these 4 are pseudogenes.

Thanks,
Shaun



-- 
http://sjackman.ca/
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