Question: How To Perform Gene Prediction In A De-Novo Genome Assembly
5
gravatar for kate.sosa
7.6 years ago by
kate.sosa50
kate.sosa50 wrote:

Hi!

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

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

ADD COMMENTlink modified 5.2 years ago by Michael Dondrup47k • written 7.6 years ago by kate.sosa50
1

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

ADD REPLYlink written 7.6 years ago by Razzmataz30
11
gravatar for a.zielezinski
7.6 years ago by
a.zielezinski9.1k
a.zielezinski9.1k wrote:

I highly recommend this outstanding review: Yandell, M., & Ence, D. (2012). A beginner’s guide to eukaryotic genome annotation. Nature Reviews Genetics, 13(5), 329–342. doi:10.1038/nrg3174

ADD COMMENTlink written 7.6 years ago by a.zielezinski9.1k
1
gravatar for sentausa
7.6 years ago by
sentausa640
France
sentausa640 wrote:

This review paper might be helpful too if you work with bacteria: Stothard P., Wishart D.S. Automated bacterial genome analysis and annotation (2006) Current Opinion in Microbiology, 9 (5), pp. 505-510.

ADD COMMENTlink modified 7.6 years ago • written 7.6 years ago by sentausa640
1
gravatar for tplsmith
7.6 years ago by
tplsmith10
Nebraska
tplsmith10 wrote:

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.

ADD COMMENTlink written 7.6 years ago by tplsmith10
0
gravatar for Lee Katz
7.6 years ago by
Lee Katz3.0k
Atlanta, GA
Lee Katz3.0k wrote:

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.

ADD COMMENTlink written 7.6 years ago by Lee Katz3.0k
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