GMAP

GMAP stands for Genomic Mapping and Alignment Program. It is a command-line software tool used to map and align messenger RNA (mRNA), expressed sequence tag (EST) and other transcript sequences to a reference genome. GMAP is designed to produce spliced alignments that reflect intron-exon structure, enabling accurate transcript-to-genome placement that supports genome annotation and transcriptome analysis.

Key features of GMAP include its use of a genome index and dynamic programming to perform splice-aware alignments. It can handle long transcripts and complex alternative splicing, recognizing canonical and noncanonical splice sites, and reporting intron boundaries along with alignment quality metrics. GMAP is capable of aligning sequences with mismatches and small gaps and is particularly well-suited for mapping full-length cDNAs or long RNA reads to large genomes. The tool is designed to integrate into annotation pipelines and can provide output that supports downstream annotation and comparative analyses.

GMAP has been widely adopted in genome annotation workflows to map transcripts to newly assembled genomes, aid in gene model construction, and assist in identifying novel splice variants. It is often used in conjunction with companion tools to build and refine gene annotations, and to validate transcript models derived from RNA sequencing experiments.

Availability and use: GMAP is distributed as a free, open-source software package for Unix-like systems. It requires a reference genome sequence and a set of transcript sequences as input, and produces mapped alignments along with exon-intron structure information suitable for integration into annotation and analysis pipelines.