Question: In search for a tool to assemble different digests
gravatar for paul75
3.9 years ago by
Vienna, Austria
paul750 wrote:

I am new in this job, but my problem is as old as proteomics: I have a (small mixture of) protein(s) that were digested with 4 different endoproteinases and then sequenced via mass-spectrometry. Now I'm looking for a tool that aligns the peptides of the 4 digests and not, as all the tools I found, the peptides within a digest against each other. So the result should be one (or a small number of) sequence of the original protein(s). Or have I just not found the right mode to run programs like clustal, mafft ...? Thx.

Update: Apparently, there seem to exist two main algorithms to do the job: Overlap-Layout-Consensus and de Bruijn Graph

Are they suited to assemble peptides too, or only genomes? Has anyone experience with implementations of them?

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by paul750

Somethings here help?

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by genomax80k

I'm afraid not. I don't need a DB-query. I need the aminoacid-sequnce of an unknown Protein, which is not found in a DB. But thanks anyway.

ADD REPLYlink written 3.9 years ago by paul750
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