est2genome WS (husar)

est2genome WS (husar) aligns expressed sequence tags (ESTs) to unspliced genomic DNA to support gene prediction by accommodating large introns and recognizing conserved donor/acceptor splice site sequences.

Key Features:

• Handling Large Introns: Accommodates large intronic regions during alignment that many traditional methods cannot manage.
• Splice Site Recognition: Detects conserved donor and acceptor splice site sequences at intron/exon boundaries to improve alignment accuracy.
• Memory Efficiency: Uses a memory-efficient algorithm enabling alignment of very large genomic DNA sequences without excessive memory use.
• Smith–Waterman Adaptation: Employs a modified Smith–Waterman dynamic programming approach tailored for spliced EST versus genomic DNA local alignments.
• Scoring System: Implements configurable scoring with default match score +1, mismatch penalty -1, and a configurable indel penalty.

Scientific Applications:

• Gene Prediction: Facilitates identification of genes within uncharacterized genomic DNA by aligning spliced ESTs to genomic sequences.
• Genomic Annotation: Assists annotation of large-scale eukaryotic genomes, particularly those with extensive intronic regions.

Methodology:

Alignment uses a modification of the Smith–Waterman dynamic programming algorithm adapted for spliced EST/genomic alignments with default scoring match +1, mismatch -1 and a configurable indel penalty; in workflows genomic DNA can be screened against dbEST using BLASTN to identify candidate ESTs which are then realigned with est2genome_ws_husar.