gmap_snpindex

gmap_snpindex constructs SNP index files and supports mapping single nucleotide polymorphisms (SNPs) to reference genomes for SNP-aware cDNA alignment and variant analysis.

Key Features:

• SNP indexing: Builds index files for known SNPs to enable variant-aware mapping.
• cDNA-to-genome alignment: Leverages GMAP's cDNA-to-genome alignment capabilities to identify gene structure in the presence of polymorphisms and sequence errors without relying on probabilistic splice site models.
• Minimal sampling strategy: Uses a minimal sampling strategy for genomic mapping.
• Oligomer chaining: Employs oligomer chaining for approximate alignment.
• Sandwich dynamic programming: Applies sandwich dynamic programming (DP) for splice site detection.
• Microexon detection and testing: Identifies microexons and applies statistical significance testing.
• High splice-site accuracy: Demonstrates >99.3% correct splice-site identification on sequences with 1–3% random mutations.
• Performance: Achieves several-fold speed improvements compared to BLAT and GeneSeqer.

Scientific Applications:

• SNP analysis: Supports identification of genetic variants that may contribute to disease or phenotypic diversity by indexing and mapping SNPs.
• cDNA alignment and gene structure analysis: Enables precise alignment of cDNA sequences to reference genomes to study gene expression and splicing.
• Integration with next-generation sequencing: Provides accurate alignments for large datasets generated by next-generation sequencing technologies for downstream variant and transcript analyses.

Methodology:

Implements a minimal sampling strategy, oligomer chaining for approximate alignment, sandwich dynamic programming for splice site detection, and microexon identification with statistical significance testing.