Types of file formats

Tue Feb 4 15:56:00 EST 1992

In message <3300.9202041204 at crc.ac.uk>, pwoollar at crc.ac.uk (Peter Woollard)
> for any details of the "NBRF RELATE" program and where to obtain it.

The now somewhat out-of-date RELATE program is still distributed on the PIR
program tape.  It is a local similarity searching program using the Fitch
method.  The program is described in the following reference.

author = "Margaret O. Dayhoff and Winona C. Barker and Lois T. Hunt",
title = "Establishing homologies in protein sequences",
year = 1983,
pages = "524-545",
booktitle = "Methods of Enzymology",
editor = "C. H. W. Hirs and S. N. Timasheff",
publisher = "The Academic Press",
address = "New York"}

It is described in more detail in a document file that can be obtained by
sending a mail message consisting of the command
(in the body of the message, not just on the "SUBJECT:" line) to

The following programs are also available from the PIR either through our
on-line service or on the PIR program distribution tape (those preceded by
an "*")

1. Database Access and Retrieval Programs
 INQ         Access to newly entered data (daily update)
*NAQ         Nucleic Acid Query (nucleic acid sequence databases, one at a time)
*PSQ         Protein Sequence Query (protein sequence databases, one at a time)
 XQS         Experimental Query System
               (simultaneous access to protein & nucleic acid databases)

2. Search Programs and Commands
 FASTA       Revised Pearson rapid homology search program
*FASTP       Pearson rapid homology search program (proteins)
*FASTN       Pearson rapid homology search program (nucleic acids)
 HIGHCOMP    Search for segments of similar composition
*ISEARCH AMB Search specifying allowed alternative residues
*RDF         Pearson program to evaluate significance of FASTP results
*SEARCH      Search database for similar segments
 scan        PSQ/XQS command for rapid location of exactly matching segments
 match       PSQ/XQS command to search for segments, allowing wildcards and

3. Global Similarity Programs
*ALIGN       NBRF Needleman-Wunsch implementation
 COMPARE     NBRF comparison of two sequences
 MTXCOR      Reisner-Westwood protein correlation

4. Local Similarity Programs
*DOTMATRIX   Fitch method with graphic output
 MTXANL      Reisner-Bucholtz method
*RELATE      Fitch method
 SEQHP       Goad-Kanehisa method (IDEAS)

5. Prediction Programs
 ALOM        Membrane-spanning segments prediction (IDEAS)
*CHOFAS      Chou-Fasman secondary structure prediction (IDEAS)
 DELPHI      Garnier secondary structure prediction (IDEAS)
 HPLOT       Hydrophobicity plot (IDEAS)
*PRPLOT      Protein plot (hydrophobicity, hydrophilicity, etc.)

6. Alignment Programs
 ALNED       Interactive alignment editor
 ALNINDEX    Lists alignment files

For information about PIR services send the commands
  HELP On-Line_Access
  HELP PIR_Distribution

Peter also asked
> I would be grateful if someone could tell me what the following
> file format initials stand for:-

MDL Molfile --- The Molecular Design Ltd. CHEMLAB and related programs
  use a molecular description MOL file.
  Molecular Design, Limited
  2132 Farallon Drive
  San Leandro, CA  94577

MM2 --- The Molecular Mechanics II (now superseded by MM3) program of
  Dr. Norman L. Allinger
  Department of Chemistry
  University of Georgia
  Athens, GA  30602

SMILES --- the molecular structure single string descriptor used by the
  MEDCHEM software of Daylight Chemical Information Systems.
  Daylight Chemical Information Systems
  3951 Claremont St.
  Irvine, CA  92714

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

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