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This Week in Nucleic Acids Research: Apr 17, 2014

Researchers from Belgium and Hungary present a web server for predicting and profiling protein backbone movements based on their amino acid sequence. The method, known as DynaMine, uses statistical analyses and available chemical shift data to produce a residue-level look at these protein dynamics, making it possible to compare different parts of the protein itself. "Through this web server, we aim at providing molecular biologists with an efficient and easy to use tool for estimating the dynamical characteristics of any protein of interest," the study's authors say, "even in the absence of experimental observations."

A Washington University-led team introduces the multiplexed direct genomic selection, or MDiGS, approach for finding copy-number variants, SNPs, and small insertions and deletions. According to the its developers, the multiplexed, targeted sequencing method picks up new SNPs, CNVs, and indels with the help of biotinylated bacterial artificial chromosome capture, pooled capture methods, and multiplexed sequencing on Illumina's MiSeq instrument. For example, the researchers demonstrated the feasibility of using MDiGS to see recurrent chromosomal duplications and small deletions in selected chromosomal regions captured from the genomes of hundreds of individuals with congenital lower limb disorders.

Belgian and Colombian researchers describe their novel sequence capture method and data filtering scheme for simultaneously seeing thousands of tandem repeats in the human genome. The team applied the large-scale analysis approach to profile tandem repeat patterns in the genomes of individuals from a three-generation family. As they report in the Nucleic Acids Research, the investigators detected a de novo variant in the family. They also determined that a significant proportion of the tandem repeats detected in the family — some 7.6 percent — were slightly distinct from those described in the human reference sequence.