SyMAP

SyMAP maps syntenic relationships between sequenced chromosomes (pseudomolecules) and FPC physical maps and computes synteny blocks for comparative genomics analyses.

Key Features:

• Supported inputs and comparisons: Compares sequenced genomes (pseudomolecules) and FPC physical maps, including genome-to-map and genome-to-genome comparisons.
• Synteny block computation: Uses MUMmer to compute raw hits between two genomes and clusters those hits into candidate synteny blocks.
• Annotation-aware filtering: Clusters and filters raw hits using optional gene annotations to refine synteny blocks.
• Synteny algorithm: Identifies duplicated regions and aggregates them into larger-scale synteny blocks while allowing intervening micro-rearrangements.
• Region-level alignments: Produces detailed alignments of hits aligned to gene annotations for local analysis of syntenic regions.

Scientific Applications:

• Genome duplication analysis: Investigation of whole-genome and segmental duplication events and their structural consequences.
• Differential gene loss: Analysis of post-duplication gene retention and loss patterns across genomes.
• Transitive homology and comparative genomics: Comparative analyses of homologous regions among species such as sorghum, maize, and rice.

Methodology:

Computes raw nucleotide-level hits with MUMmer, clusters and filters hits using optional gene annotations, and applies a synteny algorithm that detects duplicated regions and forms larger synteny blocks while permitting intervening micro-rearrangements.