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location Cambridge, MA
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seen Oct 1 at 21:54

Dec
17
comment Is there a PSI-BLAST for nucleotide sequences?
I need a bit more tinkering time
Dec
12
comment Is there a PSI-BLAST for nucleotide sequences?
That's exactly the situation I'm facing. My bacterial small RNA genes of interest are indeed noncoding.
Dec
12
comment Is there a PSI-BLAST for nucleotide sequences?
Ok, but the problem with this is it assumes conservation based on the coded protein sequence, not the nucleotide sequence. I suppose it will get some of the distant homologs, but: a) it wouldn't be optimal b) it might be weirdly biased (if that matters)