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."