e-mail submission of sequences

POSTMAST at GUNBRF.bitnet POSTMAST at GUNBRF.bitnet
Fri Jan 10 00:11:00 EST 1992


In message <9201091730.AA09176 at genbank.bio.net> "gustilo at pobox.upenn.edu" asked
> I was wondering if there is an e-mail address for the submission of sequences
> for the BLAST and fasta programs.
As Mr. Tao was kind enough to mention, the PIR Network Server can perform a
FASTA search against the PIR Protein Sequence Databases for submitted protein
or nucleotide sequences.  Requests should be directed to FILESERV at GUNBRF on
BITNET as commands or files (for BITNET nodes only), or in the body of e-mail
messages.

The SEARCH command has two formats.
  SEARCH     parameters    sequence

   or

  SEARCH     parameters
  sequence
  END SEARCH

The SEARCH command will allow a sequence to be compared in a FASTA search
(see W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448) with the PIR
databases.  You may send either protein or nucleotide sequences, however
only the PIR protein sequence databases (PIR1, PIR2, PIR3, and NRL_3D)
will be searched.  Nucleotide sequences you send will be translated in
six reading frames according to a selectable genetic code, and those
translated protein sequences will be compared against the PIR protein
sequence databases.

There are two optional parameters for the SEARCH command, KTUP and NUC.
The KTUP parameter sets the ktup value for the FASTA program.  The NUC
parameter specifies that the sequence is a nucleotide sequence, and can
select the genetic code to be used for the translation of that sequence.

Use the HELP SEARCH KTUP or HELP SEARCH NUC commands to get more information
on using these parameters.  Use the HELP SEARCH EXAMPLE command to see sample
formats.

By sending the command
  HELP topic
help is available on the following topics for PIR database access and services.

  ACCESSION                HOST                     SEND
  AUTHOR                   INDEX                    SPECIES
  BASES                    JOURNAL                  SUGGEST
  DEPOSIT                  KEYWORD                  SUPERFAMILY
  FEATURE                  On-Line_Access           TAXONOMY
  Gateway_Access           PIR_Distribution         TITLE
  GET                      QUIT
  Help_en_Espanol          RETURN
  Help_en_francais         SEARCH

------------------------------------------------------------------------
                                 Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Identification Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMASTER at GUNBRF.BITNET




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