We can now do nucleotide BLAST searches. I've been running this for a while on real data and it doesn't seem to have any problems and has found several tRNAs. The only drawback is that it requires some kind of protein BLAST to be performed first - I'm not sure why, but I suspect that some of the data structures only operate on neighborhoods and those only get created when ORFs are identified. If there's a way to make it so we can do blastn independent of blastp that would be ideal, but isn't a priority for our own projects.
We can now do nucleotide BLAST searches. I've been running this for a while on real data and it doesn't seem to have any problems and has found several tRNAs. The only drawback is that it requires some kind of protein BLAST to be performed first - I'm not sure why, but I suspect that some of the data structures only operate on neighborhoods and those only get created when ORFs are identified. If there's a way to make it so we can do blastn independent of blastp that would be ideal, but isn't a priority for our own projects.