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This Week in Nucleic Acids Research: May 30, 2013

Researchers from DSM Nutritional Products in Switzerland and the University of Oslo's Natural History Museum present a mapping-based scheme for deciphering mitochondrial genome sequence data in silico from next-generation sequencing data, even in the absence of an existing reference sequence. The group's mitochondrial baiting and iterative mapping, or MITObim, approach proved useful for putting together mitochondrial genomes for Gyrodactylus thymalli and G. derjavinoides, fish parasites that live on the surface of European grayling and rainbow trout, respectively. In their subsequent experiments, the researchers gleaned mitochondrial sequence and/or barcode information about the fish hosts, too. And their simulations suggest MITObim could be applicable to metagenomic or pooled sequence data.

An Argentina-led team has come up with a web server to spell out co-evolution patterns in proteins with multiple sequence alignment data represented as circos plots. The investigators outline the method — known as the mutual information server to infer co-evolution, or MISTIC — in an early, online study in Nucleic Acids Research. "[T]he MISTIC server allows [the user] to integrate sequence and structure information contained in [a multiple sequence alignment] in a comprehensive, compact, visually rich manner that enables the user to extract essential information in terms of networks, conservation and structure for any subset of residues of interest guiding the identification of functionally important residues in a protein," study authors say.

A study by researchers based in the US, Ireland, and Russia looks at evolutionarily conserved reading frame transitions present in prokaryotic genomes. The team brought together data from more than 1,100 existing prokaryotic genomes, using a frameshift prediction program called GeneTack to see such transitions in hundreds of thousands of genes. Genes within that set were further classified by folding in information on frameshift conservation and predicted protein similarity to one another. From there, researchers narrowed in on 4,730 frameshift transition-containing genes that have apparently undergone recoding — a collection of genes they mined further for additional functional experiments.