Looking tools for genes annotation
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19 months ago
Rima ▴ 20

Hi everyone,, I'm looking for free tools to define genes functions of bacteria (enzymatic functions) and similarities with known genes, I'm not a big fan of BLAST ! thank you in advance Best regards, Rima

Genome annotation • 1.6k views
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Needs to clarify the question here. What types of data do you have? What is the purpose of these tools etc?

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i search tools with bigger databases ! i m studing genes functions to provide an explanation for biosynthetic pathways of bioactive molecules ! manual search takes a lot of time ! I have Nucleotide sequence !

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Did you try RAST

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yes i used RAST it is limited !

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why are you not a big fan of BLAST?

it is the most used (and likely best) tool for such analyses and I can't think of any valid alternatives, except different 'flavours' of the same basic idea .

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InterProScan?

What's your problem with BLAST and sequence searches anyway?

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because it only BLASTS with NCBI-deposited data

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that is not entirely correct, BLAST can run with any database you have (and formatted for usage with blast)

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19 months ago
Juke34 7.8k

Maybe FA-nf, annocript Or sma3s

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19 months ago
Mensur Dlakic ★ 23k

One of the most widely used tools for prokaryotic genome annotation is prokka. It requires only a (meta)genome sequence, and when installed properly on a modern computer (8+ CPUs) it will fully annotate a prokaryotic genome in under 10 minutes. However, it will require additional hidden Markov model databases such as Pfam and TIGRFams, which did not come standard last time I checked.

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OP is asking for functional annotation I think.

And yes, prokka does that also to some extent but this issue might not be the most appropriate use of prokka

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yes of course i m asking for functional annotation ! is there some one who do genome mining ? I can predict manually but it takes me a lot of time to search several databases, sometimes they don't share nucleotide sequences on public... there is no direct link with genomic, chemical or functional data... in most cases chemists, biologists, bioinformaticians... work separately... In my case I do the combination of genomic, chemical and enzymatic functions, even though I'm not a specialist in all of them ,also I don't have the facility to make comparisons using connected libraries !

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prokka and the auxiliary programs assign tRNAs, rRNAs, ncRNAs, genes, CRISPR arrays. Then it makes a proteome from gene predictions, and to majority of proteins assigns a clearly defined functions such as ABC transporter or DNA binding protein. In addition, to most of the enzymes it will assign EC numbers. That is what I consider functional annotation and exactly what the OP asked. Now, the OP could have put all the details from their very last post into the original question, and that would have avoided all these extra questions we have been asking. Regardless, I still think prokka-annotated genomes are by far the best starting point for any downstream functional analysis of prokaryotes, especially given a very modest time investment.