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Fast And Accurate Method To Identify Genes In Whole Genome

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

genome genes
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updated by Michael Dondrup Michael Dondrup • written by H@rry • H@rry

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

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written by Neilfws Neilfws

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.

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written by H@rry • H@rry

you have to use the search term "gene prediction"

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written by Michael Dondrup Michael Dondrup

1 answer

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

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written by zam.iqbal.genome zam.iqbal.genome

By any such method I meant both fast and accurate btw

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written by zam.iqbal.genome zam.iqbal.genome

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).

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written by Giulietta - Ensembl Helpdesk Giulietta - Ensembl Helpdesk

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

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written by H@rry • 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.

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written by H@rry • H@rry

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