The GENOA genome annotation script [71] was used to align spliced cDNA and EST sequences to the human genome. GENOA uses BLASTN to detect significant blocks of identity between repeat-masked cDNA sequences and genomic DNA, and then aligns cDNAs to the genomic loci identified by BLASTN using the spliced-alignment algorithm MRNAVSGEN [71]. This algorithm is similar in concept to SIM4 [72] but was developed specifically to align high-quality cDNAs rather than ESTs and thus requires higher alignment quality (at least 93% identity) and consensus terminal dinucleotides at the ends of all introns (that is, GT..AG, GC..AG or AT..AC). EST sequences were aligned using SIM4 to those genomic regions that had aligned cDNAs. Stringent alignment criteria were imposed: ESTs were required to overlap cDNAs (so that all the genes studied were supported by at least one cDNA-genomic alignment); the first and last aligned segments of ESTs were required to be at least 30 nucleotides in length, with at least 90% sequence identity; and the entire EST sequence alignment was required to extend over at least 90% of the length of the EST with at least 90% sequence identity.
