Biomedical Engineering Reference
In-Depth Information
Tools
Although general-purpose pattern-matching tools can be used in search engines and data-mining
applications, nucleotide and polypeptide sequence alignment applications generally dictate the use of
bioinformatics-specific tools. As illustrated in
Table 8-4
, in addition to the sequence alignment tools
designed for nucleotide and polypeptide pattern alignment, there are support utilities for format
conversion, sequence editors, and protein and nucleotide databases.
Table 8-4. Sequence Alignment Tools. These examples typify the dozens of
pattern-matching tools available to the bioinformatics community.
Tool
Examples
Nucleotide Pattern Alignment
BLASTN, BLASTX, TBLASTX, DotLet, BALSA
Polypeptide Pattern Alignment
BLASTP, PHI-BLAST, PSI-BLAST, Smith-Waterman, ScanPROSITE,
ExPASy, DotLet, BALSA
Utilities
READSEQ, Text Editors
Protein Sequence Databases
SWISS-PROT, TrEMBL, PROSITE, BLOCKS
Nucleotide Sequence Databases GenBank, Entrez Nucleotide Database
Sequence Editor
CINEMA, GeneDoc, MACAW
Nucleotide Pattern Matching
BLAST
The best known and most used nucleotide pattern-matching programs are the original Nucleotide-
Nucleotide BLAST—sometimes referred to as BLASTN—and its derivatives. In addition to the most
recent version of BLAST, two popular derivatives are BLASTX (Nucleotide Query BLAST) and TBLASTX
(Nucleotide Query-Translated Database).
Figure 8-14
shows the Web interface to NCBI's BLASTN,
developed for nucleotide-nucleotide pattern matching.
Figure 8-14. NCBI's Nucleotide-Nucleotide BLAST (BLASTN) Web Interface.
