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Abstract
'BLAST 2 Sequences', a new BLAST-based tool for aligning two protein or nucleotide
sequences, is described. While the standard BLAST program is widely used to search
for homologous sequences in nucleotide and protein databases, one often needs to compare
only two sequences that are already known to be homologous, coming from related species
or, e.g. different isolates of the same virus. In such cases searching the entire
database would be unnecessarily time-consuming. 'BLAST 2 Sequences' utilizes the BLAST
algorithm for pairwise DNA-DNA or protein-protein sequence comparison. A World Wide
Web version of the program can be used interactively at the NCBI WWW site (http://www.ncbi.nlm.nih.gov/gorf/bl2.++
+html). The resulting alignments are presented in both graphical and text form. The
variants of the program for PC (Windows), Mac and several UNIX-based platforms can
be downloaded from the NCBI FTP site (ftp://ncbi.nlm.nih.gov).