Protein sequence mapping to genome

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lanna
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Protein sequence mapping to genome

Postby lanna » Mon Apr 06, 2015 1:59 pm

Hi,

I'm trying to find a way to map some protein sequences to the human genome, ideally something similar to the visual results done on the article "A draft of the human proteome" by Kim et al. (2014). I have the peptide evidence for the sequences as well, in case there is no reliable method of mapping the protein sequences to the human genome.

I'm aware of SAM files you can make with GMAP, but I'm not sure if I can use protein or peptide sequences for that. And yes tBLASTn will get me the translated frames but it seems to be really difficult to get a reliable result with the matches to several chromosomes and genome locations.

Any help is appreciated. Thanks in advance.

Zhang
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Postby Zhang » Tue Apr 07, 2015 7:19 am

How about use the protein database which is translated from genome? Such as Ensembl. Once you identified your peptide/protein through database search, you know exactly which transcript or gene that was encoded in the genome.

Otherwise, you can BlastP your protein/peptide sequences against the Ensembl databas, then get a similar result.



lanna wrote:Hi,

I'm trying to find a way to map some protein sequences to the human genome, ideally something similar to the visual results done on the article "A draft of the human proteome" by Kim et al. (2014). I have the peptide evidence for the sequences as well, in case there is no reliable method of mapping the protein sequences to the human genome.

I'm aware of SAM files you can make with GMAP, but I'm not sure if I can use protein or peptide sequences for that. And yes tBLASTn will get me the translated frames but it seems to be really difficult to get a reliable result with the matches to several chromosomes and genome locations.

Any help is appreciated. Thanks in advance.

Christopher
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Joined: Thu Dec 27, 2012 12:26 pm

Postby Christopher » Tue Apr 07, 2015 1:54 pm

I have used this package in R successfully: http://www.bioconductor.org/packages/release/bioc/html/proBAMr.html.

You can interface the results with a regular viewer, such as IGV (https://www.broadinstitute.org/igv/).


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