Question: How To Map Peptides To Genomic Locations (Hg19)
1
gravatar for Hmm
5.8 years ago by
Hmm500
Hmm500 wrote:

Is there a reliable tool to map the following sample peptides to genomic locations:

NMGGPYGGGNYGPGGSGGSGGYGGR
SQSSGSSATHPISVPGAR
HTGPNSPDTANDGFVR
NMGGPYGGGNYGPGGSGGSGGYGGR
SKSQSSGSSATHPISVPGAR
SHHAPMSPGSSGGGGQPLAR
GSGTASDDEFENLR

..... .............(many other peptides)

I am interested in the genomic coordinates such as chromosome and the start stop location of the peptide. Thanks

coordinates genomic map • 2.5k views
ADD COMMENTlink modified 5.8 years ago by SRKR180 • written 5.8 years ago by Hmm500
3
gravatar for JC
5.8 years ago by
JC8.0k
Mexico
JC8.0k wrote:

There are two strategies: 1. Search your peptides againts human proteins with blastp or blat, then convert the peptide coordinates to the genomic coordinates using exon annotation. 2. Search your peptides translated to nucleotides with tblastn against the reference genome.

ADD COMMENTlink written 5.8 years ago by JC8.0k
1
gravatar for SRKR
5.8 years ago by
SRKR180
Visakhapatnam
SRKR180 wrote:

Simply do a blastx of your genome with the peptide sequences.

  1. Convert the peptide sequences into multifasta format (you can use excel and microsoft word for this).
  2. Install command line blast. 3.Convert the peptide sequences into a blast database using the makeblastdb tool.
  3. Do a blastx of the genome against the created database.

You will get the coordinates of your peptide sequences mapped on to the genome.

ADD COMMENTlink written 5.8 years ago by SRKR180
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