What is Galahad?
GALAHAD, GrailEXP’s gene message alignment program, has three different tasks it can perform: • Read in a sequence and a Grail Exon Candidate file, search a database of partial/complete gene messages, and produce a list of gene message alignments. • Read in a sequence file only, search the entire sequence against a database of partial/complete gene messages, and produce a list of gene message alignments. • Read in a sequence file and an accession number of a partial/complete gene message and produce an alignment of the two sequences. A caveat regarding the use of the word “alignment”. Throughout this FAQ, it is said that GrailEXP produces “alignments”. What it actually provides are boundaries and scores; it does NOT display the actual bases lined up against each other and connected with little pipes. For the purposes of convenience, I use the word “alignment” nonetheless throughout this document to describe what GrailEXP’s gene message alignment program returns.
