BATS

BATS implements basic sequence-analysis algorithms for local and global alignments, statistical string-significance assessment via z-scores, and C/C++ and Perl library interfaces for integration with bioinformatics workflows.

Key Features:

• Alignment Algorithms: Local alignments via approximate string matching and global alignments using longest common subsequence (LCS) with support for affine and concave gap cost functions.
• Statistical Analysis: String-filtering routines and z-score computation to assess the statistical significance of sequence patterns.
• Extensibility: C/C++ and Perl library functions with integration into Bioperl for incorporation into existing bioinformatics workflows.

Scientific Applications:

• Genomic studies: Sequence analysis to identify conserved regions and functional motifs within genomes.
• Comparative genomics: Comparison of sequences across species to detect conserved regions and functional motifs.
• Evolutionary biology: Analysis of sequence alignments to infer evolutionary relationships among sequences.

Methodology:

Approximate string matching for local alignments; longest common subsequence (LCS) for global alignments; affine and concave gap cost functions for gap modeling; string filtering and z-score computation for statistical significance assessment.