Classifying proteins as enzymes, GPCRs, ion channels, etc.

I want to produce a simple classification of my proteins in my list based on whether they are enzymes, GPCRs, transducers, neurotransmitters, transcription factors, etc.

Is there a way to automatically generate that sort of classification? (I'm imagining of a open source tool that would take gene symbol as input and produce annotated output) .

Edson

rna-seq gene protein

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updated 10.4 years ago by DG

• written 10.4 years ago by ishengomae

2 answers

Dear,

You can try downloading the String-db (http://string-db.org/) database. Or you can extract a tabular data format for your gene of interest. Once you save the file, you can parse from this file using keywords of interest with script of your choice,

Regards,

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written 10.4 years ago by Ibrahim Tanyalcin

I'd recommend using the Gene Ontology. There are a variety of subsets and tools like Quick-GO and Goslim, as the Gene Ontology dataset includes a lot of annotations for every gene. Assuming of course you are talking about gene lists from a model organism, or at least just dealing with orthologs of genes that are well described in a model organism. You'll have to explore the Gene Ontology a bit, as it is heirarchical annotation, and decide what level of annotation you need to apply to get the gene type definition you want.

Another alternative might be to annotate them into functional groups with PantherDB or a similar tool.

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written 10.4 years ago by DG

Gene Ontology is a really nice idea! Below you can find an initial reference to it.

GOstat: find statistically overrepresented Gene Ontologies within a group of genes. [Bioinformatics. 2004]

This is their web-site:

http://gostat.wehi.edu.au

You will find many others on this site, and among them there is the reference already provided by Dan Gaston.

http://www.geneontology.org

You can also try pFam for many different options:

http://pfam.xfam.org/

As well as InterPro, InterProScan sequence search:

http://www.ebi.ac.uk/interpro/search/sequence-search

Have I understood it correctly and you have initally some gene sequences in nucleotides?

In this case you will need to translate them first. I'm not sure I know a lot of tools

starting from sequence in nucleotides and finishing with the protein annotation.

Only this one works like that: http://geneontology.org/.

If you prefer something different, you will need some translation tool.

There are a lot of translation tools, you will find them here:

https://www.google.ru/#newwindow=1&q=gene+translation+tool

Good luck!

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written 10.4 years ago by natasha.sernova