How To Perform Gene Prediction In A De-Novo Genome Assembly
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12.3 years ago
kate.sosa ▴ 50

Hi!

I have any questions about gene prediction in de novo genome assembly.

How can I do it? What ideas do you have?

gene denovo annotation gene-prediction • 7.6k views
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Could an admin or the original poster add tags for 'denovo', 'annotation', and 'gene-prediction'? Thanks!

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12.3 years ago
tplsmith ▴ 10

For bacterial genomes we have used DIYA very successfully (http://gmod.org/wiki/DIYA) in a linux environment, implemented in a semi-automated pipeline as part of the MiniLims package from BioTeam. The output is a GenBank-ready file that can be analyzed in any viewers that can interpret such files.

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12.3 years ago
Lee Katz ★ 3.2k

This is a really general question. You can research gene prediction by looking at review articles on gene prediction (none I know off the top of my head) or by going to a pipeline-centric article. Such pipelines include PGAAP, RAST, BASys, Clovr, and CG-Pipeline.

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