We have one prominent request for nucleotide-to-protein alignment in Bowtie. I'm giving it priority 3 to make it clear that it's behind paired-end and gapped alignments in terms of priority.
PADUA has this functionality now. No plans to implement it within Bowtie, since good tools already exist and protein datasets tend not to be nearly as big as sequencing datasets.
Ben
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PADUA has this functionality now. No plans to implement it within Bowtie, since good tools already exist and protein datasets tend not to be nearly as big as sequencing datasets.
Ben