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Adaptive Local Realignment of Protein Sequences.

08:00 EDT 11th June 2018 | BioPortfolio

Summary of "Adaptive Local Realignment of Protein Sequences."

While mutation rates can vary markedly over the residues of a protein, multiple sequence alignment tools typically use the same values for their scoring-function parameters across a protein's entire length. We present a new approach, called adaptive local realignment, that in contrast automatically adapts to the diversity of mutation rates along protein sequences. This builds upon a recent technique known as parameter advising, which finds global parameter settings for an aligner, to now adaptively find local settings. Our approach in essence identifies local regions with low estimated accuracy, constructs a set of candidate realignments using a carefully-chosen collection of parameter settings, and replaces the region if a realignment has higher estimated accuracy. This new method of local parameter advising, when combined with prior methods for global advising, boosts alignment accuracy as much as 26% over the best default setting on hard-to-align protein benchmarks, and by 6.4% over global advising alone. Adaptive local realignment has been implemented within the Opal aligner using the Facet accuracy estimator.

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Journal Details

This article was published in the following journal.

Name: Journal of computational biology : a journal of computational molecular cell biology
ISSN: 1557-8666
Pages:

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Medical and Biotech [MESH] Definitions

The excision of in-frame internal protein sequences (INTEINS) of a precursor protein, coupled with ligation of the flanking sequences (EXTEINS). Protein splicing is an autocatalytic reaction and results in the production of two proteins from a single primary translation product: the intein and the mature protein.

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A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).

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