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This Week in Nucleic Acids Research: Jun 11, 2014

In the early edition of Nucleic Acids Research, a Virginia Tech team describes a server called EvoCor — developed for figuring out the functional relationships between genes using phylogenetic patterns, evolutionary relationships, and gene expression information. By assessing sequence divergence data and gene expression profiles in tissues of interest, the researchers say, EvoCor can offer clues about genes governing related functional processes. These and other aspects of the tool can contribute to unbiased functional predictions about biological outcomes associated with various genes, they note.

Harvard University researchers introduce an online tool for designing genome editing experiments using TALEN or CRISPR/Cas9-based approaches. The web resource, dubbed CHOPCHOP, includes sequence alignment algorithms and gene visualization tools meant to make it easier for investigators to come up with candidate genome editing constructs. For instance, study authors say, CHOPCHOP makes it possible to visualize various restriction sites and primer possibilities, while assigning quality scores to target sites at different spots in the genome.

Investigators from the University of Kent's Centre for Molecular Processing present a scheme for predicting the functional consequences of non-synonymous SNPs. By incorporating protein sequence and structural feature cues into the non-synonymous variant analysis, their Variant Modeller, or VarMod, method provides clues to understanding genotype effects on phenotype, the study authors note. Their proof-of-principle analysis of 3,000 such variants suggests VarMod predicts protein function and structural effects with accuracy that's on par with that offered by the PolyPhen-2 tool.