RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints

Abstract

RE-MuSiC is a web-based multiple sequence alignment tool that can incorporate biological knowledge about structure, function, or conserved patterns regarding the sequences of interest. It accepts amino acid or nucleic acid sequences and a set of constraints as inputs. The constraints are pattern descriptions, instead of exact positions of fragments to be aligned together. The output is an alignment where for each pattern (constraint), an occurrence on each sequence can be found aligned together with those on the other sequences, in a manner that the overall alignment is optimized. Its predecessor, MuSiC, has been found useful by researchers since its release in 2004. However, it is noticed in applications that the pattern formulation adopted in MuSiC, namely, plain strings allowing mismatches, is not expressive and flexible enough. The constraint formulation adopted in RE-MuSiC is therefore enhanced to be regular expressions, which is convenient in expressing many biologically significant patterns like those collected in the PROSITE database, or structural consensuses that often involve variable ranges between conserved parts. Experiments demonstrate that RE-MuSiC can be used to help predict important residues and locate phylogenetically conserved structural elements. RE-MuSiC is available on-line at http://140.113.239.131/RE-MUSIC.

CORAL-M: Heuristic coding region alignment method for multiple genome sequences

“…In this paper, we want to find the potential function sites for EV71 and CA16 strains by comparing with Sabin strains using CLUSTALW, RE-MuSiC [14] At first, we compare the strains of Sabin1-PV1, Sabin2-PV2, and Sabin3-PV3 by using these tools. The pairs of aligning codons corresponding to the known function sites of Sabin1-3 are shown in Table 1.…”

CSA-X: Modularized Constrained Multiple Sequence Alignment

“…Chung et al introduced RE-MuSiC for constrained multiple sequence alignment that accepts regular expression constraints [8]. It identifies the regions matched by the regular expression and generates an alignment where these matching regions get aligned.…”

“…RECSA [5] and the other algorithm for the constrained alignment of multiple sequences [4] by Arslan are not available as implemented programs. Furthermore, Chung et al [8] wrote in their paper that these algorithms only report the alignment score and not the complete alignment. The tool proposed by Chung et al RE-MuSiC, does report full alignments and scores, but accepts only a subset of regular expressions as input, and does not always align the regions matched by the regular expression constraint, as discussed in detail in Section 2.9.…”

“…Because of this, Tsai et al [50] proposed MuSiC, a web server, that allows constrained alignment of sequences. But many biologically important motifs such as those listed as regular expressions in the PROSITE [25] database cannot be formulated as constraints according to the convention followed by MuSiC [8]. To solve this issue, Arslan [5] and Chung et al [9] introduced alignment algorithms that accept regular expression constraints.…”

“…To solve this issue, Arslan [5] and Chung et al [9] introduced alignment algorithms that accept regular expression constraints. Then, Chung et al proposed RE-MuSiC [8], an extension to their previous work [9], to support multiple sequences and multiple constraints. In that work, they used sequence motifs found in PROSITE as regular expression constraints to improve the quality of alignments.…”