November 2008 Archives

To celebrate the day of my birth, MBE issued the advanced access version of my manuscript: “Problems and solutions for estimating indel rates and length distributions” (pdf) and the supplement.

Well I’ve sent my stuff off to the publisher, so I figure that I’ll share the abstract with y’all.

Cartwright RA. Problems and solutions for estimating indel rates and length distributions. Molecular Biology and Evolution. (in press)

Insertions and deletions (indels) are fundamental but understudied components of molecular evolution. Here we present an expectation-maximization algorithm built on a pair hidden Markov model that is able to properly handle indels in neutrally evolving DNA sequences. From a dataset of orthologous introns, we estimate relative rates and length distributions of indels among primates and rodents. This technique has the advantage of potentially handling large genomic datasets. We find that a zeta power-law model of indel lengths provides a much better fit than the traditional geometric model and that indel processes are conserved between our taxa. The estimated relative rates are about 12–16 indels per 100 substitutions, and the estimated power-law magnitudes are about 1.6–1.7. More significantly, we find that using the traditional geometric/affine model of indel lengths introduces artifacts into evolutionary analysis, casting doubt on studies of the evolution and diversity of indel formation using traditional models and invalidating measures of species divergence that include indel lengths.

Texas Tech drops, and Texas maintains a lead over Oklahoma.

I found out today that my manuscript, “Problems and Solutions for Estimating Indel Rates and Length Distributions” was accepted for publication in Molecular Biology and Evolution. Yay! I can update that line in my CV.

Speaking of CVs, I’ve applied to over thirty open faculty positions this year. I have no idea how competitive I am for any of them.

I’m not doing a computer poll this week because nothing really happened last week. With the Texas Tech-Oklahoma show down this week, the top of the rankings is going to get very interesting.

And we got snow flurries today.

And Fallout 3 rocks.

Texas Tech’s blowout of Oklahoma State still wasn’t strong enough into jump them in top two. They still jumped ahead of a Bama team still looking for a second blow out victory over a top team.

Florida takes over the top spot after beating Georgia and having Texas lose. Texas still has enough quality wins to stay at #2. Alabama and Texas Tech are a bit lower because they don’t have as many huge victories as the other two. If Texas Tech can win big against one of its future opponents, they’ll move up. Alabama might need to blow out LSU or Auburn if it wants to finish the regular season at number 1.