November 2008 Archives

The Big Three-O

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.

RankTeamRecordQuality
1Florida10-18.2616
2Texas10-18.1485
3Southern Cal9-18.0230
4Oklahoma10-17.8945
5Alabama11-07.6695
6Penn State11-17.6300
7Texas Tech10-17.5917
8Utah12-07.4408
9Georgia9-27.2727
10Ohio State10-27.1104

In Pressed

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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.

RankTeamRecordQuality
1Florida8-18.5213
2Texas9-18.2336
3Southern Cal8-18.2192
4Texas Tech10-08.0160
5Alabama10-07.8028
6Oklahoma9-17.7687
7Utah10-07.6122
8Penn State9-17.5863
9Georgia8-27.4115
10North Carolina7-27.3216

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.

RankTeamRecordQuality
1Florida7-18.5834
2Texas8-18.2730
3Southern Cal7-18.0990
4Penn State9-07.9110
5Alabama9-07.8763
6Texas Tech9-07.7709
7Oklahoma8-17.7539
8Georgia7-27.4821
9Utah9-07.3119
10Missouri7-27.1778

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