Question: Protein grouping tool
0
gravatar for pisiposo84
3.3 years ago by
pisiposo8450
pisiposo8450 wrote:

Hi,

Does anyone know a tool that can compute the list of protein groups (following the occam' s rule) using as input a list of peptide sequences?

All the proteomics software I know do this only 'internally' on the list of peptides identified by MS analysis. I am looking for something that allows me to submit a list of peptides I want, regardless if they have been identified or not...

Thanks

ADD COMMENTlink modified 3.1 years ago by prvst0 • written 3.3 years ago by pisiposo8450

I have this as part of an old perl script, using EnsEMBL proteins as reference. It would probably need adapting but I can dig it up if nobody comes with a ready to use solution.

ADD REPLYlink written 3.3 years ago by Jean-Karim Heriche23k

That would be great. I am currently basing my 'analysis' on UniProt entries, whereas the list of peptides is a two columns lists, with the column 1 containing the peptide sequence and column 2 the accession number of the protein the peptide belongs to... but I guess I can be very flexible with the input data.

ADD REPLYlink written 3.3 years ago by pisiposo8450

What kind of 'groups' are you after? If you just want to group/cluster the proteins by sequence, you can do this with the CD-HIT suite of tools.

ADD REPLYlink written 3.1 years ago by Joe18k
0
gravatar for prvst
3.1 years ago by
prvst0
United States
prvst0 wrote:

You can try ProteinProphet, it's part of the Trans-Proteomics Pipeline (TPP)

ADD COMMENTlink written 3.1 years ago by prvst0
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