Character generation

Bioinformatics Zen has a funny post on the World of Bioinformatics Quest: Character generation. It made me laugh.

Alignment Uncertainty

Today in Science, Wong et. al. has a brief three page report entitled, “Alignment Uncertainty and Genomic Analysis”. In the same issue (pg 416; doi 10.1126/science.1153156) Rokas writes a perspective on Wong’s report. [Ironically, Rokas' perspective is probably near the same amount of text as Wong's report since Wong includes two large figures.]The report makes a simple assertion, “methods applied to the analysis of genomic data do not account for uncertainty in the sequence alignment.” They then show, by applying seven different popular alignment programs to protein sequences from seven yeast species, that uncertainty in the alignment can lead to problems, including different alignments giving different conclusions.

Morpheus Unbound

A year ago, Arthur Lander published a review in Cell entitled “Morpheus Unbound: Reimagining the Morphogen Gradient”. It’s an articulate review of morphogen gradients — their formation, function, and regulation. He highlights the history of morphogen study and in so doing paints a picture of both how different perspectives have enriched the field and how it has evolved over time. It is a great read, heavily recommended.

Structural Variation in the Human Genome

Back in mid December I attended a talk by Evan Eichler entitled, “Structural Variation in the Human Genome”. Evan gave an excellent talk focusing on his lab’s recent work on identifying the regions of the genome which change in structure and content very quickly. In short, identify length variations within the human genome. His talk broke down into two major components:

1. Identify duplicated regions associated with phenotypes
2. Catalog normal structural variation in the genome

I’ll go into more details on both below the fold …