PECAN

PECAN generates consistency-based base-pair whole-genome alignments and consistent homology maps for pairwise and multiple-genome comparative analyses.

Key Features:

• Consistency-based alignment methodology: PECAN employs a consistency approach to produce coherent homology maps across multiple genomes.
• Colinear segment partitioning (Enredo): Input genomes are partitioned into colinear segments using Enredo to manage genomic rearrangements, including duplications.
• Base-pair level alignment: PECAN generates detailed base-pair resolution alignments for each colinear segment.
• Homology map generation: PECAN produces consistent homology maps that enable the transformation of one genome into another.
• Scalability for large-scale genome-wide alignments: PECAN is designed to handle large-scale genomic data across multiple mammalian genomes.

Scientific Applications:

• Comparative genomics: PECAN provides consistent and detailed homology maps to support comparative studies across species for evolutionary and functional analyses.
• Genomic rearrangement analysis: The partitioning and alignment approach supports analysis of complex genomic rearrangements and duplications.
• Data integration with Ensembl: Alignments produced by PECAN are integrated into the Ensembl genome browser for downstream use.

Methodology:

Genomes are partitioned into colinear segments using Enredo, then PECAN performs consistency-based base-pair level alignment of those segments to produce consistent homology maps.