Research article

A new protein linear motif benchmark for multiple sequence alignment software

Emmanuel Perrodou^1,2,3 , Claudia Chica⁴ , Olivier Poch^1,2,3 , Toby J Gibson⁴ and Julie D Thompson^1,2,3

¹  Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Structural Biology and Genomics, F-67400 Illkirch, France

²  Institut National de la Santé et de la Recherche Médicale (INSERM), U596, F-67400 Illkirch, France

³  The Centre National de la Recherche Scientifique (CNRS), UMR7104, F-67400 Illkirch, France; Université Louis Pasteur, F-67000 Strasbourg, France

⁴  European Molecular Biology Laboratory, Meyerhofstraße 1, 69012 Heidelberg, Germany

author email corresponding author email

BMC Bioinformatics 2008, 9:213doi:10.1186/1471-2105-9-213

Published:	25 April 2008

Abstract

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 and align LMs. The reference alignments are organised into different test sets representing real alignment problems and contain examples of experimentally verified functional motifs, extracted from the Eukaryotic Linear Motif (ELM) database. The benchmark has been used to evaluate and compare a number of multiple alignment programs. With distantly related proteins, the worst alignment program correctly aligns 48% of LMs compared to 73% for the best program. However, the performance of all the programs is adversely affected by the introduction of other sequences containing false positive motifs. The ranking of the alignment programs based on LM alignment quality is similar to that observed when considering full-length protein alignments, however little correlation was observed between LM and overall alignment quality for individual alignment test cases.

Conclusion

We have shown that none of the programs currently available is capable of reliably aligning LMs in distantly related sequences and we have highlighted a number of specific problems. The results of the tests suggest possible ways to improve program accuracy for difficult, divergent sequences.