DBGET - Access Bioinfomatics Databases at GenomeNet

DBGET is an integrated bioinfomatics database retrieval system at GenomeNet. The WWW interface is available at http://www.genome.ad.jp/dbget/dbget.html. A set of client Unix commands that provides a simple command line interface to these databases are installed at UCSC. These commands are particularly useful for retrieving current database entries. For example, the command

        bget pdb 1adb >1adb.pdb

will retrieve the entire 1adb PDB file. The command

        bget pdb -f 1adb >1adb.seq

will retrieve the 1adb sequence in FASTA format. To get a list of available databases, use the binfo command.

The DBGET manual is a useful starting place. NetDBget refers to the client commands we have installed locally.

DBGET Client Commands

bget - Get entries from a database.
dbget - Synonym for bget
bfind - Find entries in a database with matching character patterns in the definition line.
bman - Retrieve documentation on DBGET commands and databases
binfo- List database versions and statistics.
blink - Follows links in database entries. I haven't been able to get this to do anything useful.
btit - I don't have a clue what commandthis does.

Local contact: markd