What is a gene message alignment?
A gene message alignment is an alignment between a genomic sequence (in which genes are chopped up into pieces) and a gene message (in which a gene is a single contiguous piece of DNA built from spliced together exons). It differs from a regular global alignment because there is additional information that can help with the alignment process, most notably that the internal “edges” of each alignment piece should fall on standard splice site (GT….AG) boundaries. A gene message alignment program aligns a gene message with a genomic sequence such that the exon/intron boundaries are clearly identified.
