Hi,
What would be a good tool to use to query 200-400bp intergenic sequences from one mammalian species to the reference genome of another, something like human-mouse distance? Blast?
Just to clarify, I don't have the reference genome for one species with the query 200-400bp sequences, but I do have the reference genome for the target species.
At UCSC Table Browser there are data of BLAT alignments between species.
Currently I'm working comparing BLAT and GMAP results, and it seems GMAP is more tolerant to mismatch than BLAT and it finds about 30% more alignments than BLAT. So if you want to do this kind of alignments, you should try GMAP.
You can download here: http://research-pub.gene.com/gmap/
I would use BLAT if you want to search the whole genome for intergenic homology in mammals but do not have a whole genome alignment. BLAT's chaining of HSPs will make it very easy (where possible) to identify your hit. Is this a one off or are you doing this en masse?
It turns out I needed something more flexible with gaps than BLAT. I tried BLASTN and it seems to do the trick: blastn -E 10 -B 100 -filter dust -RepeatMasker -W 9 -M 1 -N -1 -Q 2 -R 1
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This are tens of thousands, so it's not millions, like NGS sequences. The fact that these are non-coding intergenic regions, many of them probably evolving neutrally makes me wonder if I need a method that will still be sensitive when the target hit has been disrupted by small or medium indels. Is blat good for that?