Question: IGV and proteomics
0
gravatar for mdfardin374
11 months ago by
mdfardin3740 wrote:

Hello, I have a list of peptides and I am interested in visualizing their location in the genome so that gene structure could be revised. How do I get to know whether the peptide is in intron or in UTR or overlapping two exons?

genome • 265 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by mdfardin3740

IGV is not really related to the question you are asking, is it?

You should probably add some information about where these peotides come from? What is their length? You can do blat searches against the genome to find their location easily (as long as they are long/unique). Once you find their location you could then map that information on to annotation.

ADD REPLYlink written 11 months ago by genomax85k

Would this be of help? https://www.rcsb.org/pages/help/featureView

From your question it's not really clear what type of data you have (i.e. do you have a list of (arbitrary) peptide identifiers, or Uniprot accession numbers of the proteins they belong to etc.)

ADD REPLYlink written 11 months ago by Friederike5.7k

Actually, it is a list of novel peptides identified from MS/MS database search.

ADD REPLYlink written 11 months ago by mdfardin3740

does that mean you do not know which proteins they belong to?

ADD REPLYlink written 11 months ago by Friederike5.7k
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