Question: Mapping peptide to the source genomic region
0
gravatar for genie66
4.1 years ago by
genie6620
United States
genie6620 wrote:

I have a list of peptide sequences, their respective protein names, their start and end co-ordinates in their protein sequences. Now I wanted to map them back to genomic source and get the genomic start and end co-ordinates(preferably exons) . I have tried several tools like proteogenomic mapping tools but no luck. Peptide atlas could able to provide the exonic co-ordinates but only one peptide is possible at a time, I have hundreds of peptides! Is there is any other way to do this! Please help me out! Thanks!

peptide mapping • 2.0k views
ADD COMMENTlink modified 2.4 years ago by microbe7730 • written 4.1 years ago by genie6620
1
gravatar for microbe77
2.4 years ago by
microbe7730
USA
microbe7730 wrote:

Might be too late, but this is how to do it! 1. make a six frame peptide library from you genome (all possible peptides), I use 10 aa +, for 4.5M bp bacterium about 0.25M peptides 2. use this as a reference to get all peptides that map to your possible peptides 3. Get a fasta file that contains all the genome nucleotide sequence (this should be one entry fastafile that contains ALL nucleotides 4. make a nucleotide blast database using makeblastdb command from local blast installation 5. align your peptides to the genome database using tblastn: tblastn -query <your peptide="" fasta="" file=""> -db <your genome="" database="" (these="" are="" three="" files,="" just="" use="" name="" without="" extension)="" -out="" <name="" of="" the="" out="" file="" you="" want=""> -outfmt 6 (the -outfmt 6 will give you tabular results) -max_target_seqs <1 or more, use 1> (not sure about this option though double check!) -evalue 0.001 (to eliminate partial alignment)

  1. open file in excel and only keep genome name (useually NC_xxxx), start, stop. Save this file as .bed which will be readable in almost all genome browsers (I use IGB)
  2. The code that makes six frames is in python. I will paste the code hereunder:

better to find the code here: https://github.com/microbe777/fasta2six_frames

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by microbe7730
0
gravatar for raunakms
4.1 years ago by
raunakms1.0k
Vancouver, BC, Canada
raunakms1.0k wrote:

using tools like tBLASTn could be a good starting point where it compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands).

ADD COMMENTlink written 4.1 years ago by raunakms1.0k
0
gravatar for Siva
4.1 years ago by
Siva1.6k
United States
Siva1.6k wrote:

You could try Scipio which uses blat to search a query protein sequence against its genome. It outputs the intron/exon boundaries and splice sites.

ADD COMMENTlink written 4.1 years ago by Siva1.6k
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