Types of file formats

POSTMAST at GUNBRF.bitnet POSTMAST at GUNBRF.bitnet
Tue Feb 4 15:56:00 EST 1992


In message <3300.9202041204 at crc.ac.uk>, pwoollar at crc.ac.uk (Peter Woollard)
asked
> 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The now somewhat out-of-date RELATE program is still distributed on the PIR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.

@inbook{P77,
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
  SEND RELATE.DOC
(in the body of the message, not just on the "SUBJECT:" line) to
  FILESERV at GUNBRF.BITNET

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
               mismatches

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
to FILESERV at GUNBRF.BITNET.

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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