Databases for Bioinformatics

Prof. Gene Cooperman, College of Computer Science

OVERVIEW

Bioinformatics databases provide for gene and protein sequencing are among the fastest growing databases that exist. Searching these databases efficiently and with high selectivity is essential for their use. The database labs will provide experience in using database tools ranging from the very fast, but inexact BLAST\256 (Basic Local Alignment Search Tool) through the slower, but more accurate HMMER, and on to PDB. BLAST\256 (Basic Local Alignment Search Tool) is a package for rapidly searching genome and protein databases distributed by NCBI (National Center for Biotechnology Information). HMMER is a package for creating and using Hidden Markov Model profiles for DNA and protein sequence analysis. PDB (Protein Data Bank) is a database of the 3-dimensional structure of proteins.