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The now somewhat out-of-date RELATE program is still distributed on the PIR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
