Filtering Spliced Alignment Before Build Gene Models
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12.8 years ago
Plantae ▴ 390

I try to annotate one new genome, several sources of evidence were used, include ESTs (PASA), homolog protein aligments (Genewise) and abinito predictions,

The problem is that i got several gene models for each locus, for example, GeneWise alignment create >500,000 gene models, I run wise after blast, but I do not filter the blast result (all blast hits were used for genewise alignment).

I guess that blast results should be filtered before running wise alignment, but I don't know routine paramers that can be used to filter blast results (eg. identity, alignment length)

dose anybody have some opinion about the routine process in gene structure prediction?

gene annotation filter • 2.0k views
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Genewise - now that takes me back a good 10-12 years!

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