How To Map Peptides To Genomic Locations (Hg19)
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1
Entering edit mode
8.2 years ago
Hmm ▴ 500

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

map genomic coordinates • 3.3k views
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3
Entering edit mode
8.2 years ago
JC 12k

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.

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1
Entering edit mode
8.2 years ago
SRKR ▴ 180

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.

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