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This Week in Nucleic Acids Research: Apr 15, 2015

A team from Spain and France provides details on a Transitive Consistency Score, or TCS, web server designed to assess multiple protein sequence alignments, including comparisons done in a phylogenetic context. The approach, which uses information from the stability of multiple sequence alignments to estimate local reliability of these alignments, appears to compare favorably with other alignment evaluation schemes, the study's authors argue. "Its systematic usage should help decrease the uncertainty resulting from the use of different alignment methods," they write, "and therefore increase the robustness and reproducibility of biological results established on the basis of [multiple sequence alignment] modeling."

Austrian researchers introduce a strategy for calling variants in repetitive regions of the genome that relies on the use of a genetic variation "thesaurus." The computational approach clusters potential variants within such tricky-to-align regions, the team says, using the variant thesaurus to tally up regions with similar sequences. In their proof-of-principle application of this method, the investigators aligned simulated or real reads — which included sequences from exome sequencing of healthy human cells or breast cancer cells lines — to the human reference genome, using the thesaurus-based scheme to see previously unappreciated elements in repetitive parts of the genome.

An analytical approach known as SplicePie appears to show promise for characterizing alternative splicing events from RNA sequencing data generating at different stages in the splicing process, according to a study by researchers in the Netherlands. Based on SplicePie analyses of these so-called pre-, intermediate-, and post-splicing patterns, the team was able to begin looking at the order in which different splicing events occur, producing a more nuanced look at the sequential, non-sequencing, and/or recursive splicing events that influence intron use.