How To Perform Gene Prediction In A De-Novo Genome Assembly

Question

[kate.sosa]

Hi!

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

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

[Razzmataz]

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

Answer 1

[Andrzej Zielezinski]

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

Answer 2

[sentausa]

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.

Answer 3

[tplsmith]

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.

Answer 4

[Lee Katz]

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.