I am looking at over 10 million reads in the form of fasta. I want to determine if each sequence has a portion of a tRNA sequence. I've been using tRNAscan-SE but this takes a very long time for a large number of reads since it was designed for contigs.
Scanning for HMMs is very quick. Is there a tool that does this or a HMM set that I can use to say "read_X has or does not have a tRNA hit"
I looked in the source code of tRNAscan-SE and didn't notice any HMMs.