Fast And Accurate Method To Identify Genes In Whole Genome

Question

[H@rry]

Hi,

I am looking for some fast and accurate method for the identification of genes in whole genome. I am using HMM based profiles and searched in protein database of respective genomes but unable to identify correctly (few genes returning). Blast is also good but I am wondering if some statistical method exist to do the task.

Thanks

[Michael]

you have to use the search term "gene prediction"

[Neilfws]

There are lots of tools available to do this, depending on the organism. For example, GeneMark, Glimmer.

[H@rry]

Thanks alot. I am using Plant fungal genome as a search again some particular gene called resistance genes. I am not sure if some tool is available for this purpose.

Answer 1

[zam.iqbal.genome]

What type of organism? I don't think there exists any such method for vertebrates. You could send an email to the Ensembl help desk for advice. But according to their webpages: http://www.ensembl.org/info/genome/genebuild/genome_annotation.html it takes them 4 months to run the gene prediction pipeline.

For bacteria, you could look up Prokka: http://www.vicbioinformatics.com/software.prokka.shtml

[Giulietta - Ensembl Helpdesk]

Indeed, the Ensembl pipeline is quite involved, but it has to be to yield high quality gene and transcript models for vertebrates. There is a two-day gene annotation course at end of September in Cambridge, UK, so if you do think you might be interested and you are in the country, send our helpdesk an email asking to be registered (helpdesk at ensembl.org).

[H@rry]

Well, I am willing to attend attend the course and I will send my enquiry to helpdesk.

[zam.iqbal.genome]

By any such method I meant both fast and accurate btw

[H@rry]

Thanks alor for your information, but I am using plant fungal genome as a search against some particular gene called resistance genes. I would like to identify all the R genes which possess characteristic domain such as Leucine repeat and NBS. That is why I am searching some method for the mining of these kind of gene families in fungal genomes.