MacVector enables you to use the BLAST (Basic Local Alignment Search Tool) heuristic search algorithm to search sequence databases available on the National Center for Biotechnology Information (NCBI) server, to find sequences that are similar to either nucleic acid or protein query sequences. Currently, homologs to a query sequence can be determined using the following search types:
- BLASTN compares a nucleotide query sequence against a nucleotide sequence database.
- BLASTP compares an amino acid query sequence against a protein sequence database.
- BLASTX compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database.
- TBLASTN compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands).
- TBLASTX compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.
All of the above search types use the newest BLAST algorithms (BLAST 2; Altschul et al. 1997). All except TBLASTX offer gapped alignment searching. Because they yield more biologically meaningful results, gapped searches are enabled by default.
These five programs ascribe significance to their findings using the statistical methods of Karlin and Altschul (1990, 1993). PSI-BLAST, PHI-BLAST, and 2-sequence BLAST searches are not currently available.