MAFin

MAFin enables efficient motif detection and conservation analysis in Multiple Alignment Format (MAF) files for genomic and proteomic comparative research.

Key Features:

• K-mer Search: Searches aligned sequences using user-specified k-mers.
• Regular Expression Search: Searches one or more patterns using regular expressions.
• Position Weight Matrix Search: Searches using predefined Position Weight Matrices.
• Conservation Analysis: Detects motif instances and calculates conservation across aligned sequences.
• Conservation Percentage: Calculates conservation levels based on the number of matches relative to motif length.
• Statistical Interpretation: Provides a set of statistics for interpreting each motif's conservation level.
• Export Formats: Exports detected motifs in JSON and CSV formats for downstream analyses.
• Multithreading: Enables multithreaded search of conserved motifs.

Scientific Applications:

• Comparative Genomics: Identifies conserved motifs in whole genome alignments to understand functional and evolutionary relationships.
• Comparative Proteomics: Identifies conserved motifs in proteome alignments to understand functional and evolutionary relationships.

Methodology:

MAFin searches Multiple Alignment Format files using three approaches: user-specified k-mers, regular expressions, or predefined Position Weight Matrices. Upon motif detection, the tool calculates conservation across aligned sequences and computes a conservation percentage based on matches relative to motif length.