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
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
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