POWERBLAST - A NEW NETWORK BLAST APPLICATION FOR INTERACTIVE OR AUTOMATED SEQUENCE-ANALYSIS AND ANNOTATION

As the rate of DNA sequencing increases, analysis by sequence similari ty search will need to become much more efficient in terms of sensitiv ity, specificity, automation potential, and consistency in annotation. PowerBLAST was developed, in part, to address these problems. PowerBL AST includes a number of options for masking repetitive elements and l ow complexity subsequences. It also has the capacity to restrict the s earch to any level of NCBI's taxonomy index, thus supporting ''compara tive genomics'' applications. Postprocessing of the BLAST output using the SIM series of algorithms produces optimal, gapped alignments, and multiple alignments when a region of the query sequence matches multi ple database sequences. PowerBLAST is capable of processing sequences of any length because it divides long query sequences into overlapping fragments and then merges the results after searching. The results ma y be viewed graphically, as a textual representation, or as an HTML pa ge with links to GenBank and Entrez. For matching database sequences, annotated features are superimposed on the aligned query sequence in t he output, thus greatly increasing the ease of interpretation. Such fe atures may be used for automated annotation of new sequence because Po werBLAST output in ASN.1 form may be ''dragged and dropped'' into NCBI 's Sequin program for sequence annotation and submission. PowerBLAST i s capable of analyzing and annotating a 100-kb query in 60 min on NCBI 's BLAST server.