RE-MuSiC

RE-MuSiC performs constrained multiple sequence alignment using user-defined regular-expression patterns to align amino acid and nucleic acid sequences and identify conserved motifs, structural consensuses, and functionally important residues.

Key Features:

• Constrained Alignment: Uses regular expressions to specify constraints that define conserved blocks or motifs within sequences.
• Input Flexibility: Accepts amino acid and nucleic acid sequences together with pattern descriptions that can represent complex conserved motifs or structural elements rather than only exact positions.
• Optimized Alignment Output: Produces alignments optimized to align occurrences of each specified pattern coherently across all input sequences.
• Biological Pattern Support: Expresses PROSITE-like patterns and structural consensuses with variable ranges between conserved parts to aid prediction of important residues and conserved structural elements.

Scientific Applications:

• Functional residue prediction: Identifies and aligns conserved motifs to support prediction of functionally important residues in proteins and nucleic acids.
• Conserved structural element identification: Detects conserved structural consensuses across sequences to inform studies of evolutionary conservation and structural constraints.
• Domain and active-site analysis: Aligns sequences based on known conserved patterns to facilitate analysis of protein domains and active sites.

Methodology:

Applies regular-expression-specified constraints within the multiple sequence alignment procedure and optimizes alignments so that occurrences of each pattern are aligned coherently across sequences.