NCBI maintains Genomic BLAST pages for >100 organisms shown in the Map Viewer. By default, genomic BLAST searches the genomic sequence of an organism, but additional databases are also available, such as the nucleotide and protein RefSeqs annotated on the genomic sequence, as well as sets of sequences such as Expressed Sequence Tags (ESTs) that are mapped to the genomic sequence. The default search program for the NCBI Genomic BLAST pages is MegaBLAST (15), a faster version of standard nucleotide BLAST designed to find alignments between nearly identical sequences, typically from the same species. It is available through a separate web interface that handles batch nucleotide queries and can be used to search the rapidly growing Trace Archive as well as the standard BLAST databases. For rapid cross-species nucleotide queries, NCBI offers Discontiguous MegaBLAST, which uses a noncontiguous word match (16) as the nucleus for its alignments. Discontiguous MegaBLAST is far more rapid than a translated search such as blastx, yet maintains a competitive degree of sensitivity when comparing coding regions.
