DBGET - bfind command

NAME
     bfind - find entries in a database with  matching  character
     patterns in the definition line

SYNOPSIS
     bfind dbname [ -Cnow ] pattern ...

DESCRIPTION
     bfind searches for sequence entries of a given database with
     matching  character  patterns  in  the definition line.  The
     definition line usually contains a brief description of  the
     content  of  each  entry.   The  argument  dbname  may  be a
     reserved keyword for the database.  Currently available pub-
     lic databases are:

          dbname        database
          ------------  --------------------------------------
          genbank       GenBank nucleic acid sequence database
          genbank-today Current GenBank including daily updates
          embl          EMBL nucleic acid sequence database
          pir           PIR protein sequence database
          nbrf          (Same as above)
          swissprot     SWISS-PROT protein sequence database
          prf           PRF protein sequence database
          pdb           Brookhaven Protein Data Bank
          pdbstr        Re-organized Protein Data Bank
          prosite       Dictionary of protein sites and patterns
          epd           Eukaryotic Promoter Database
          omim          Online Mendelian Inheritance in Man
          ligand        Ligand Chemical Database for Enzyme Reaction
          litdb         Literature Database compiled by PRF
          pmd           Protein Mutant Database
          aaindex       Amino Acid Index Database


     By default the  search  is  case-insensitive;  namely,  both
     upper and lower cases may be matched to a given pattern. The
     routine reports the entry names and definitions found.

     When multiple patterns are given,  bfind  performs  the  AND
     operation;  definition  lines  containing  all  of  them are
     reported.  Use -o option when the OR operation is required.

OPTIONS
     -C    Perform case-sensitive search.

     -n    Search definition lines not containing  the  following
          pattern.

     -o    Search definition lines containing either the  preced-
          ing pattern or the following pattern.

     -w    Treat the following pattern as a word; search only the
          pattern separated by special characters or spaces.

FILES
     At the Supercomputer Laboratory, the public  database  names
     are  defined by the environmental variables such as the fol-
     lowing:
          setenv genbank /bio/db/genbank/genbank

EXAMPLES
     Search 'zinc finger', 'zinc-finger', 'Zinc finger', etc.

          example% bfind genbank zinc finger

     Search only 'Cytochrome c'.

          example% bfind swissprot -C 'Cytochrome c'

     Search immunogloblulin (abbreviated as Ig in the  PIR  data-
     base) gamma or delta chain.

          example% bfind pir -w ig gamma -o delta

SEE ALSO
     bget