I need to find exons that are conserved between multiple species, such as human and mouse. I have tried to
liftOver, but even though when I tweak the parameters to make it more sensitive, I lose most of my exons. To complement this approach, I am trying
blat and it seems that is working fine. My only problem is that this approach sounds quite old fashion to me, does someone know the other way find conserved exons across species? I am sure there are many ways to do this, I am interested to know which would be your choice as a bioinformatician.
PD: At the moment I only want to map
20967 exonic sequences and blat is fast enough when I do:
blat $Genome $Query $out -t=dna -q=dna -stepSize=5 -minScore=0 -minIdentity=0 -repMatch=1000000 -noHead
Perhaps even if you know if a better configuration of blat to do such mapping, would be very useful to star exploring this.
Update: With liftOver 856 mouse exons that overlap with annotated exons, whereas with blat I was able to find 11215 mouse exons that are conserved in human. Blat was not a bad option after all!