Splign (28) (www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi) is a utility for computing cDNA-to-genomic sequence alignments that is accurate in determining splice sites, tolerant of sequencing errors and supports cross-species alignments. Splign uses a version of the Needleman–Wunsch algorithm (29) that accounts for splice signals in combination with a compartmentalization algorithm to identify possible locations of genes and their copies. A link to download a standalone version designed for large-scale processing is provided on the Splign web page.
