How is GrailEXP structured?
GrailEXP consists of three binaries wrapped by a single Perl script which calls the binaries in the appropriate way based on the user’s requests. The first of these programs is the exon prediction program (called Perceval, and containing the latest version of the Grail suite, including repetitive finding, exon prediction, CpG island location, and other features). The second of these programs is the gene message alignment program (called Galahad), which can search against any number of databases, align with a single mRNA/EST, either relying on Grail or Genscan exons as a seed or not. The final program is the gene assembly program (called Gawain), which assembles genes from the EST alignments, recognizes alternative splicing, finds 5′ and 3′ untranslated regions, and predicts polya and promoter elements. The programs are called through a single, easy-to-use Perl script called ‘grailexp’.
