A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

Abstract

Multiple comparison or alignmentof protein sequences has become a fundamental tool in many different domains in modern molecular biology, from evolutionary studies to prediction of 2D/3D structure, molecular function and inter-molecular interactions etc. By placing the sequence in the framework of the overall family, multiple alignments can be used to identify conserved features and to highlight differences or specificities. In this paper, we describe a comprehensive evaluation of many of the most popular methods for multiple sequence alignment (MSA), based on a new benchmark test set. The benchmark is designed to represent typical problems encountered when aligning the large protein sequence sets that result from today's high throughput biotechnologies. We show that alignmentmethods have significantly progressed and can now identify most of the shared sequence features that determine the broad molecular function(s) of a protein family, even for divergent sequences. However,we have identified a number of important challenges. First, the locally conserved regions, that reflect functional specificities or that modulate a protein's function in a given cellular context,are less well aligned. Second, motifs in natively disordered regions are often misaligned. Third, the badly predicted or fragmentary protein sequences, which make up a large proportion of today's databases, lead to a significant number of alignment errors. Based on this study, we demonstrate that the existing MSA methods can be exploited in combination to improve alignment accuracy, although novel approaches will still be needed to fully explore the most difficult regions. We then propose knowledge-enabled, dynamic solutions that will hopefully pave the way to enhanced alignment construction and exploitation in future evolutionary systems biology studies.

A comparative analysis of multiple sequence alignments for biological data

“…In [2], families are included that are aligned with highly distant sequences. [3] contains sequences from four different families, such that the similarity between two sequences that belong to different families is less than 25%. [4] is with N/C terminal extension, and [5] contains sequences with internal insertions [15].…”

“…The new test case contains 10 reference sets with different MSA problems. This reference set of BAliBASE consists of 218 reference alignments and 17892 protein sequences [3].…”

“…One of the challenging tasks is to analyze these sequences and extract biologically significant but hidden information [2]. Construction and analysis of multiple sequence alignment (MSA) is a prerequisite in these studies and in post-genomic biological research [3].…”

“…Many sequences remain conserved throughout evolution. By highlighting these conserved regions, the motif, domain and catalytic sites of proteins can be obtained [3].…”

Maximal Information from Local Alignments

“…Alignment boundary accuracy is different from equivalent residue accuracy measured in multiple sequence alignment (MSA) (Aniba et al, 2010;Thompson et al, 2011). A MSA can be thought of as a continuation of multiple pairwise alignments; once many homologs have been identified using pairwise methods, all of the homologous sequences can then be aligned with the aim to identify equivalent residues across all of the homologs.…”