Sigma 2.0 BETA

Sigma 2.0 BETA aligns non-coding DNA sequences using a gapless local alignment approach to identify conserved fragments and regulatory sites in intergenic regions.

Key Features:

• Algorithmic Innovation: Seeks optimal gapless local alignments adapted from methodologies such as DiAlign to suit rapidly evolving non-coding DNA.
• Scoring Scheme: Evaluates alignment significance using a scoring mechanism based on lengths of aligned fragments and a background model that can be user-supplied or estimated from an auxiliary file containing intergenic DNA.
• Comparative Genomics Integration: Aligns phylogenetically related intergenic sequences to facilitate identification of regulatory sites across species.
• Performance and Sensitivity: Demonstrated, on synthetic data that mimic real scenarios, a balance of high sensitivity (aligning more bases) with filtering to minimize incorrect alignments.
• Compatibility with Motif Discovery: Alignments produced by Sigma have been used with PhyloGibbs for downstream motif finding and regulatory element discovery.

Scientific Applications:

• Comparative Genomics: Identification of conserved non-coding fragments and regulatory sites across phylogenetically related species using intergenic sequence alignments.
• Gene Regulation Studies: Preparation of alignments for downstream motif discovery and analysis of regulatory element evolution.
• Evolutionary Analysis of Intergenic Regions: Analysis of rapidly evolving non-coding DNA to investigate genetic diversity and species adaptation in non-coding genomic regions.

Methodology:

Computes optimal gapless local alignments; scores alignments by aligned-fragment lengths and a background model (user-supplied or estimated from an auxiliary intergenic DNA file); applies filtering to reduce incorrect alignments; evaluated using synthetic data.