ABMapper

ABMapper performs spliced alignment and junction site detection to accurately map RNA sequencing (RNA-seq) reads, including multi-mapping reads, for transcriptome and alternative splicing analysis.

Key Features:

• Spliced Alignment: Aligns reads across splice junctions in RNA-seq data to support detection of exon–exon boundaries and alternative splicing.
• Junction Site Detection: Identifies potential splice junction sites within sequencing reads to inform exon–intron boundary annotation.
• Handling Multi-Reads: Explores all possible alignments for reads that map to multiple genomic locations to address repetitive sequences and reduce placement ambiguity.
• Implementation and Portability: Implemented in C++ and PERL and runs on Windows, Mac OS X, and LINUX.
• Efficiency: Optimized for speed and memory efficiency to process large RNA-seq datasets.

Scientific Applications:

• Transcriptomics: Provides detailed mapping across splice junctions to support transcriptome profiling and gene expression analysis.
• Genomic Research: Enables analysis of repetitive genomic regions and loci with high sequence similarity by handling multi-mapping reads.
• Alternative Splicing Studies: Detects splice junctions and spliced alignments to identify novel splice variants and study isoform diversity.

Methodology:

Employs a specialized algorithmic approach tailored for RNA-seq that explores all potential alignments of reads, particularly those spanning splice junctions or mapping to repetitive regions.