Putative gene finding in a proteome file

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7.8 years ago

Mehmet ▴ 820

Dear All:

I have a proteome file of a non model organism. I would like to identify novel genes in the file. How can I do that?

Thank you.

RNA-Seq genome sequence gene • 1.7k views

ADD COMMENT • link 7.8 years ago by Mehmet ▴ 820

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Are these peptide fragments or longer translations from genome sequence?

ADD REPLY • link 7.8 years ago by GenoMax 141k

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translations from RNA.

ADD REPLY • link 7.8 years ago by Mehmet ▴ 820

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What do you mean by novel?

ADD REPLY • link 7.8 years ago by sentausa ▴ 650

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I mean genes which are unique to my organisms. Also, do you know how can I identify some protein related genes, such as genes related to Neuropeptides, peptides etc.?

ADD REPLY • link 7.8 years ago by Mehmet ▴ 820

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If there is a related genome available (for which a good proteome exists) then you could try to download that and then use blast searches to identify proteins that are homologous. Then for the ones that don't match anything significant you can start with widening the search out to UniProt/RefSeq databases.

There are also these resources that you can look at: http://www.peptideatlas.org/
http://www.matrixscience.com/search_form_select.html

ADD REPLY • link 7.8 years ago by GenoMax 141k

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