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BMCBI
2008

A new protein linear motif benchmark for multiple sequence alignment software

9 years 3 days ago
A new protein linear motif benchmark for multiple sequence alignment software
Background: Linear motifs (LMs) are abundant short regulatory sites used for modulating the functions of many eukaryotic proteins. They play important roles in post-translational modification, cell compartment targeting, docking sites for regulatory complex assembly and protein processing and cleavage. Methods for LM detection are now being developed that are strongly dependent on scores for motif conservation in homologous proteins. However, most LMs are found in natively disordered polypeptide segments that evolve rapidly, unhindered by structural constraints on the sequence. These regions of modular proteins are difficult to align using classical multiple sequence alignment programs that are specifically optimised to align the globular domains. As a consequence, poor motif alignment quality is hindering efforts to detect new LMs. Results: We have developed a new benchmark, as part of the BAliBASE suite, designed to assess the ability of standard multiple alignment methods to detect...
Emmanuel Perrodou, Claudia Chica, Olivier Poch, To
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2008
Where BMCBI
Authors Emmanuel Perrodou, Claudia Chica, Olivier Poch, Toby J. Gibson, Julie Dawn Thompson
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