gmap_build

gmap_build generates genome indices for GMAP and GSNAP to enable mapping and alignment of cDNA sequences to reference genomes.

Key Features:

• Efficient mapping and alignment: Enables rapid mapping and alignment of cDNA sequences to a reference genome with reduced startup time and memory requirements.
• Accurate gene structure prediction: Produces accurate gene structures in the presence of polymorphisms and sequence errors using oligomer chaining for approximate alignment and sandwich dynamic programming for splice site detection, without relying on probabilistic splice site models.
• Microexon identification: Incorporates statistical significance testing to detect microexons.
• Performance superiority: Demonstrated higher accuracy than blat and GeneSeqer, correctly identifying splice sites in over 99.3% of human mRNA sequences with 1% and 3% random mutations and achieving an error rate one-tenth that of other programs.
• Scalability and speed: Provides several-fold increases in speed relative to existing genome mapping programs, enabling large-scale genomic analyses.
• Minimal sampling strategy: Employs a minimal sampling strategy to reduce computational load while maintaining mapping accuracy.

Scientific Applications:

• Genomic Research: Facilitates precise alignment of cDNA sequences to reference genomes for studies of gene structure, expression, and regulation.
• Biomedical Research: Supports accurate gene structure and splice site identification to investigate genetic variation and its implications for health and disease.

Methodology:

Uses a minimal sampling strategy; oligomer chaining for approximate alignment; sandwich dynamic programming (DP) for splice site detection; and statistical significance testing to identify microexons.