castanyes blaves

Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes : Abstract : Nature

Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes

Very simple but elegant analysis. They used different alignment programs to check for errors, and the plots show distances from 0 to 25bp and 0 to 50bp. Say an indel is at 12bp of a mismatch: are we properly aligning the sequences? Would PRANK give different results on a set of human-chimp-orang-macaque multiple alignments compared to the pairwise alignments methods used in the paper? The results indicate that this is not a recombination effect. That's interesting. There is a pile of papers out there that relate polymorphism (and divergence?) to recombination rates. Not exactly contradictory, but interesting to see the difference in results.