Hi,
Is there any fast aligner that aligns nucleotide sequences to protein databases?
I've used blastx but blastx is too slow and takes too much memory, I'm wondering if anything like bowtie exists.
Thanks!
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Tianyang Li •
Maybe Usearch might be useful.
Apparently blat can't do this. I got this when I ran it: d and q must both be either protein or dna
A new answer brought me back to this old thread.
The error message "d and q must both be either protein or dna" is not correct; it should begin "t and q". Furthermore, this error occurs when -q=dna, not -q=dnax as I suggested. The error in the latter case is "Unrecognized combination of target and query types."
An answer in this thread suggests simply switching the -t and -q options (i.e. -q=prot -t=dnax).
Blat with options -t=prot -q=dnax gives results similar to tBLASTn but not BLASTx. Be careful during the comparisons.
The mapx command from Real Time Genomics is for this specific scenario. As well as being inherently very fast, it also supports multiple cores. It is included in our commercial RTG Metagenomics and RTG Core products, as well as the non-commercial version of RTG Core.
All true, but unfortunately it stinks at doing blastX-like searches
really? besides protein-protein searches, I understood this was one of the principal objectives of the algorithm. What do you mean?
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