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Sequence Alignment in Six Easy Steps

At his blog, Buried Treasure, Lars Juhl Jensen discusses two papers that point out possible mistakes in the current, and commonly used, sequence alignment techniques. The papers, published in Science and Nature Biotechnology, describe how uncertainties in multiple alignments can lead to errors in different phylogenetic trees, and discover that the most commonly used substitution matrix, BLOSUM62, was calculated wrongly. Jensen details his own methods of how to avoid mistakes, including using programs like "Gblocks to remove the ambiguous parts of their alignments before moving on to constructing phylogenetic trees," he writes. "Upon casual reading of these publications, one could get the idea that over a decade of work based on alignments, sequence similarity searches, and molecular evolution is wrong. Fortunately, this does not appear to be the case."

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.