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Old 04-24-2012, 08:33 AM   #1
NYGAWI
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Location: Madison, WI

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Default Software for mapping translated nucleotide sequences to a local reference database

Hello All,
I am wondering if anyone knows of a program for mapping translated nucleotide sequences to a reference protein database? I have between 300k and 1 million nucleotide sequences per sample (so 1.8 to 6 million translated sequences) that I would like to map against a viral protein refseq database I downloaded from NCBI. I am currently using CLC genomics workbench for analyzing my nexgen data and can map the trimmed nucleotide sequences to the reference viral nucleotide database from NCBI. However, since I am doing virus discovery work, I would also like to map protein to protein as well. By the way, we can BLAST all our sequences, but the mapping is a quick way (at least at the nucleotide to nucleotide level) to look for obvious similarities between our output and reference sequences. Thanks!
-Sam

Last edited by NYGAWI; 04-24-2012 at 08:35 AM. Reason: Typo in title
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Old 04-24-2012, 08:46 AM   #2
Richard Finney
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Jim Kent's "blat" program ...

http://genome.ucsc.edu/goldenPath/help/blatSpec.html

See the -prot parameter
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Old 04-24-2012, 09:05 AM   #3
NYGAWI
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Richard,

Thanks for the suggestion. Looking at the BLAT website, it is written that mapping is limited to 80% identity for proteins. Is this true in practice? For our work, the desire to map proteins is motivated by the possible presence of sequences that show much greater divergence from references (say 30 to 70% identity to reference sequences). Any thought are appreciated! Thanks,

-Sam
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