MJB1@phoenix.cambridge.ac.uk (02/02/89)
2/2/89 [1] 11:32 am
PUBLIC DOMAIN MOLECULAR BIOLOGY SOFTWARE AVAILABLE FROM THE
COMPUTER LABORATORY.UNIVERSITY OF CAMBRIDGE.
The software listed below is available without charge. Send details of the
items required with the specified number of discs (5.25"
360K for IBM PC SOFTWARE, 3.5" 800K for Apple Macintosh software, no need to
format discs) to:
David Judge,
Room 204,
Department of Genetics,
University of Cambridge,
Tennis Court Road,
Cambridge CB2 3H.
Telephone (0223) 333614
Electronic mail: DPJ10@UK.AC.CAM.PHX
DPJ10@UK.AC.CAM.BIO
Many of the descriptions of the programs listed are based on their entries on
Dr. Christopher J. Rawlings 'Software Directory for
Molecular Biologists.' published by Macmilllan Publishers Ltd. Copies of most
of the papers mentioned below are available in
the DNA Sequencing Teaching Laboratory.
SOFTWARE FOR THE IBM PC
TITLE: Sequence (PCS), version 1.1
RECEIVED: 1984
AUTHOR: L. Mark Lagrimini, Steven T. Bretano and J. E. Donelson, University of
Iowa.
SOURCE: The authors. NO. DISCS: 2
DESCRIPTION:
With this package it is possible to: compare nucleotide sequences; compare
peptide sequences; compare sequences by dot
matrix; determine codon/trinucleotide frequency; determine nucleotide frequency
in nucleotide sequence; determine peptide
frequency in peptide sequence; edit sequence data; enter sequences manually;
invert sequences; manage communications
between computers (file transfer and terminal emulation); plot restriction maps;
predict molecular weight of peptide sequence;
predict restriction fragment size from sequence and search for
oligonucleotides/restriction sites and translation of nucleotide
sequence. Executable files only.
TITLE: MATILDA, version 1.1
RECEIVED: 24/6/88
AUTHOR: Dr. David Shalloway and Norman Deering, Pennsylvania State University.
SOURCE: MBCRR NO. DISCS: 2
DESCRIPTION:
With this package it is possible to: print maps of restriction and functional
sites for a recombinant molecule; enter and edit
restriction fragment data into a database; manage a database of recombinant
clones; manage restriction map data files and
simulate recombinant cloning to characterise a construct before actual
laboratory construction. Executable files only.
A general overview of MATILDA has been given in "DNA Data Base Management at the
Restriction and Functional Site
Level", by D. Shalloway and N. Deering (1984) Nucl. Acids Res. 12, 739-750. On
the instructions of Dr. Shalloway, a copy
of this paper will accompany each copy of the MATILDA software. Copies of
another unpublished paper by Dr. Shalloway
are available in the DNA Sequencing Teaching Laboratory.
Dr. Shalloway is currently working on MATILDA II wich will have a number of
output enhancements, will be more user
friendly and will accept sequence data directly from Genbank files. This should
be ready around the end of 1988 and will be
available for around $300. A brochure showing some of the new output formats is
available in the DNA Sequencing Teaching
Laboratory.
TITLE: Mount Sequence Analysis Tools, Version 5.01
RECEIVED: 24/6/88.
AUTHOR: Dr. David W. Mount and Bruce Conrad, University of Arizona.
SOURCE: MBCRR NO. DISCS: 1
DESCRIPTION:
This package can be used to: Compare nucleotide and peptide sequences ; create
new sequence by joining/breaking existing
ones or from overlapping regions; examine codon, dinucleotide or peptide
frequency; display hydropathy profile for peptide
sequences; enter and edit sequence data; find open reading frames; search for
restriction sites; predict restriction fragment size
from sequence; predict restriction sites from peptide sequence; reverse
translate peptide sequence; search for oligonucleotide in
peptide sequence; search for potential control sequences or repeated
sequences;search for subsequences and symmetric regions
and translate nucleotide sequence. Executable files only.
See Mount, D. W. and Conrad, B. (1986) Nucl. Acids Res. 14, 443-454.
TITLE: Cornell DNA Sequence Analysis Package.
RECEIVED: December 1987.
AUTHOR: Dr. Brian Fristensky, North Carolina State University.
SOURCE: MBCRR NO. DISCS: 5
DESCRIPTION:
With this package it is possible to: compare nucleotide sequences; compare
peptide sequences; compare sequences by dot
matrix; compare sequences for overlapping regions; create new sequences from
sequences with overlapping regions; determine
nucleotide frequency in nucleotide sequence; determine optimal alignment of two
sequences; display restriction maps; edit gel
sequence data; enter sequences manually; plot asymetric base usage; plot
nucleotide frequency distribution; plot restriction
maps; predict restriction fragment size from sequence; print sequence formatted
for publication and search for
oligonucleotides/restriction sites. The programs are written in Pascal. Source
code is supplied.
See Fristensky, Lis and Wu (1982) Nucl. Acids Res. 10, 6451-6463 and Fristensky
(1986) Nucl. Acids Res. 14, 597-610.
TITLE: MBCRR Package
RECEIVED: 24/6/88
AUTHOR: Several authors associated with the Molecular Biology Computing Research
Resource,Dana-Farber Cancer
Institute, Boston, MA.
SOURCE: MBCRR NO. DISCS: 3
DESCRIPTION:
This package contains a variety of molecular biology applications, including
programs to predict potential protein secondary
structure, search for maximum homologous common sequences between nucleic acid
or protein sequences, find the optimal
alignment between pairs of genetic sequences, format sequence files in most
formats to a form usable by the MBCRR
programs, calculate some simple statistics of nucleic acid sequences, and
extract sequences from GENBANK and other
sequence databases. Executable files and source code.
TITLE: Lipman Rapid Biosequence similarity analysis system.
RECEIVED: 24/6/88
AUTHOR: Dr. D. J. Lipman, National Institutes of Health, Bethesda and Dr. W. R.
Pearson, University of Virginia.
SOURCE: MBCRR NO. DISCS: 12
DESCRIPTION:
With this package it is possible to: search protein sequence databases for
sequences similar to a given sequence; extract
sequences from protein sequence databases into individual files; to determine
the statistical significance of sequence similarity.
The programs (FASTP etc.) are written in C. The source code is included. The
programs are accompanied by a recent version
of the PIR protein sequence database (version 17.0, with version 35.0 of the
sequences in preparation, at the time of writing)
in a suitable format. New versions of the PIR database will be made available as
we receive them.
The SWISSPROT (from EMBL) protein database (currently version 8.0) is also
available (9 discs). The PIR database is
available separately (7 discs for the main database plus 4 for the sequences in
preparation).
A version of these programs and similar programs (FASTN etc.) for DNA sequences
and databases are available from:
The Austin Code Works,
11100 Leafwood Lane,
Austin, TX 78750, USA. Tel: (512) 258-0785
The programs cost around $30, they are normally packaged with the PIR protein
sequence database ($60) or the GENBANK
DNA database on floppy discs ($150).
Dr. Pearson is now distributing the full FASTA package. These programs do
everything that FASTP and FASTN do plus
much more. Currently the FASTA package is only available directly from Dr.
Pearson. Send $60 to:
Dr. William R. Pearson
Department of Biochemistry
University of Virginia
Charlottesville, VA 22908
U.S.A.
We can provide a demonstration disc for FASTA, available on 1 disc.
For technical information about the programs, see: Pearson, W. A. and Lipmannn,
D. J. (1988) P.N.A.S. 85, 2444-2448.
TITLE: PHYLIP-Phylogeny Inference Package, version 3.1
RECEIVED: 29/6/88
AUTHOR: Dr. Joe Felsenstein, University of Washington.
SOURCE: The author. NO. DISCS: 10
DESCRIPTION:
With this package it is possible to: determine evolutionary distance between
sequences and infer a dendrogram from nucleotide
sequences. Dr. Felsenstein provides only the source code for the programs
written in Pascal. We have compiled them using
Turbo Pascal 4.0, and most of them work in a straight forward fashion as
described in the documentation provided by Dr.
Felstenstein.
Anyone who we send this package will have their address forwarded to Dr.
Felsenstein who will then keep you informed
about new releases, etc.
TITLE: PCFOLD, version 3.0
RECEIVED: 24/6/88
AUTHOR: Dr. Michael Zuker, National Research Council of Canada, Ottawa.
SOURCE: MBCRR NO. DISCS: 1
DESCRIPTION:
Performs calculations to characterise base-pairing in folded RNA molecules by
estimating the most stable structure in terms
of free-energy. Base-pair energies as well as a wide range of other parameters
are user-definable.
Written in Microsoft Fortran and assembler. Source code and executable file
are provided.
See Zuker, M. and Stiegler, P. (1981) Nucl. Acids Res. 9, 133. and Jacobson,
A.B.et. al. (1984) Nucl. Acids Res. 12, 45.
TITLE: MOLECULE & GEL, versions of 25/5/87 & 14/4/87
RECEIVED: January 1988
AUTHOR: Dr. John R. Thompson, Carnegie -Mellon University.
SOURCE: BIONET NO. DISCS: 1
DESCRIPTION:
MOLECULE will be of interest to users of Dr. Zuker's program PCFOLD (see above).
It reads the output of this program and
produces a 2D graphic representation of the structure predicted. Versions of
MOLECULE are provided for the IBM CGA, EGA
and the Hercules Monochrome graphics card.
GEL computes fragment sizes from fragment mobilities. The program is based on
the FORTRAN program described by
Schaffer and Sederoff (Anal. Biochem. 115,113-122[81]). Copies of this paper
are available in the DNA Sequencing Teaching
Laboratory.
Both programs are written in Turbo Pascal. The source code is included.
TITLE: PLASMID PAINT, version 1.1
RECEIVED: 14/3/88
AUTHOR: Dr Joe Lipsick, UC San Diego.
SOURCE: BIONET NO. DISCS: 1
DESCRIPTION:
This program will allow you to draw plasmids using an IBM PC with a CGA. It is
written in Microsoft Quick BASIC
(2.0). Executable code only.
Hopefully an EGA version of this program will be available soon.
TITLE: ALP3/ALN3, version 1.0
RECEIVED: 19/10/87
AUTHOR: Osamu Gotoh, Saitama Cancer Research Institute, Japan.
SOURCE: BIONET NO. DISCS: 1
DESCRIPTION:
This program performs "Alignment of Three Biological Sequences with an Efficient
Traceback Procedure". Uses some
implementation of the algorithm described in Gotoh, O. (1986) J. Theor. Biol.
121, 327-337. Executable files only.
TITLE: RZMAP.
RECEIVED: 24/6/88
AUTHOR: Dr. William Ralph.
SOURCE: MBCRR NO. DISCS: 1
DESCRIPTION:
A program to compute restriction maps from double digest fragment lengths. The
details of the method used are described in
Fitch, W. M. et.al. (1983) Gene 22, 9-29. Source code and executable files are
provided.
TITLE: RZMAPIN, version 1.0
RECEIVED: February 1987
AUTHOR: David Judge, Cambridge University.
SOURCE: The author. NO. DISCS: 1
DESCRIPTION:
This program will only be of interest to people using RZMAP (see above).
RZMAPIN allows the easy production of input files for analysis by RZMAP. Data
can be input as fragment lengths or as
fragment mobilities entered via the keyboard or as fragment mobilities measured
directly from an Agarose gel photograph
using a sonic digitiser (SAC Graf/Bar).
A facility for creating RZMAP input files is now provided by Dr. Ralph with
RZMAP. RZMAPIN is now only really
necessary if you want to set up RZMAP input files using a digitiser.
TITLE: READGEL, version 2.0
RECEIVED: February 1987
AUTHOR: David Judge, Cambridge University.
SOURCE: The author. NO. DISCS: 2
DESCRIPTION:
A program to input sequences from Sanger gels into disc files using a sonic
digitiser (SAC Graf/Bar). This program will be
distributed with 2 short CBT lessons. One to explain how the program and the
digitiser work and one to outline some of the
difficulties of Sanger gel interpretation.
TITLE: FRAGSIZE, version 1.0
RECEIVED: February 1987
AUTHOR: David Judge, Cambridge University.
SOURCE: The author. NO. DISCS: 1
DESCRIPTION:
A program to estimate fragment lengths from a photograph of an Agarose gel.
Mobilities may be input from the photograph
either directly, using a sonic digitiser (SAC Graf/Bar), or via the keyboard
after conventional measurement.
TITLE: SIM, version 1.0
RECEIVED: February 1987
AUTHOR: David Judge, Cambridge University.
SOURCE: The author. NO. DISCS: 2
DESCRIPTION:
A program to simulate the production and analysis of an Agarose gel. I imagine
this program will only be of interest for
teaching purposes.
Various DNA sequences, molecular weight standards and enzyme descriptions are
available to the program. From the
selection made, the program is capable of:
- producing a graphical representation of the Agarose gel that would result from
the selection and providing a facility to read
fragment mobilities from the screen is provided. Fragment lengths are
automatically estimated from the mobilities read.
- producing a restriction map for the chosen sequence and selected enzymes.
NOTE: This program requires BOTH a monochrome and a colour monitor.
TITLE: GELPROG and ROBUST
RECEIVED: April 1986
AUTHOR: Ken Merrifield and Dr. Plikaytis.
SOURCE: Ken Merrifield. NO. DISCS: 1
DESCRIPTION:
GELPROG is an agarose gel sizing program. ROBUST estimates standard curves for
protein molecular weight and linear-
duplex DNA length. See Plikaytis, B. D., et. al. (1986) Anal. Biochem. 152,
346-364.
SOFTWARE FOR THE APPLE MACINTOSH
Much of the Apple Macintosh programs we currently distribute came from Dr. Peter
Markiewicz, who distributes in the U.S.A.
and periodically sends out a software review, "MAC in Molecular Biology".
His address is as follows:
Dr. Peter Markiewicz,
Molecular Biology Institute,
UCLA,
Los Angeles, CA.
Phone: 213-825-8460
Dr. Markiewicz ported most of the programs he supplied from IBM PC versions. The
descriptions of these programs also comes
from Dr. Markiewicz.
TITLE: DNANALYZE, version 1.8
RECEIVED: April 1988
AUTHOR: Schwindinger, W. F. and Warner, J. R.
SOURCE: Dr. Peter Markiewicz. NO. DISCS: 1
DESCRIPTION:
This is a general-purpose DNA sequence analysis program derived from a version
for the IBM PC.See Nucl. Acids Res. 12,
601-604. The program reads IntelliGenetics format and simple text sequence
files. Features include: Create, clone and draw
sequence, GC/AT plot, translation, restrict sequence, codon usage, dot-matrix
homology plot, open reading frames, sequence
codon degeneracy, and others.
TITLE: MOLGENJR
RECEIVED: April 1988
AUTHOR: J. R. Lowe.
SOURCE: Dr. Peter Markiewicz. NO. DISCS: 1
DESCRIPTION:
A general-purpose DNA and protein sequence analysis program adapted from an
original program for the IBM PC. See
Federal Proceedings 45, 1852. Reads IntelliGenetics, EMBL, and plain text
sequence formats. Features: restrict DNA
sequence; double digests; search for exact DNA or protein sequence; search for
enhancer-type sequence; translate DNA
sequence; open reading frames; codon usage; ORFS is peptide file; Garnier
secondary structure prediction; Kyte-Doolittle or
Hopp-Woods hydropathy; Dna sizes from mobility; DNA concentrations from
absorbance; plus several others.
TITLE: t-RNA search programs
RECEIVED: April 1988
AUTHOR:
SOURCE: Dr. Peter Markiewicz. NO. DISCS: 1
DESCRIPTION:
A set of four programs for searching DNA sequences for prokaryotik, eukaryotic,
mitochondrial, and intron-type t-RNA
sequences. Draws aligned sequence into possible t-RNA structure.
TITLE: FASTP and THREE
RECEIVED: April 1988
AUTHOR: FASTP: Dr. D. J. Lipman and Dr. W. R. Pearson.
SOURCE: Dr. Peter Markiewicz. NO. DISCS: 5
DESCRIPTION:
FASTP compares a test peptide against the proteins in the NBRF database. Reads
BIONET (IntelliGenetics) format sequence
files. Also includes RDF, a statistics program, and Lib Prot, which extracts
sequence matches from the NBRF database.
Distributed with a recent version of the NBRF database (version 17.0 with
version 35.0 of the sequences in preparation, at the
time of writing).
The SWISSPROT (from EMBL) protein sequence database (currently version 8.0) is
also available on 4 discs. The NBRF
database is also available separately (3 discs for the main database plus 2 for
the sequences in preparation).
THREE aligns three protein sequences for maximum homology. Can read protein
sequences extracted by FASTP.
TITLE: Plasmid Draw, MacDNA, and LIGATE and SIP
RECEIVED: April 1988
AUTHOR: Plasmid Draw: Wolfram Siede; Ligate and Sip; Jenson
SOURCE: Dr. Peter Markiewicz. NO. DISCS: 1
DESCRIPTION:
Plasmid Draw makes drawings of circular or linear DNA sequences with restriction
maps. The drawings may be transferred to
other programs such as MacDraw.
MacDNA is a general-purpose DNA sequence analysis program. Lacks a 'MAC'-type
interface, file size limit of 8000 bases.
LIGATE and CIP calculate ligation reactions, and phosphatase usage in
dephosphorylation reactions.
TITLE: Digigel
RECEIVED: December 1988
AUTHOR: Hugh Salter, Cambridge University.
SOURCE: The author. NO. DISCS: 1
DESCRIPTION:
A program to read sequences from Sanger gels into disc files using a sonic
digitiser (SAC Graf/Bar).
TITLE: DNA Strider
RECEIVED: July 1988
AUTHOR: Christian Marck
SOURCE: The author. NO. DISCS: 1
DESCRIPTION:
DNA Strider is a general-purpose DNA and protein sequence analysis package. It
can be used to perform classical restriction
and translation analyses, edit sequences, graphically draw restriction maps,
hydrophobicity profiles, and the codon adaptation
index. DNA Strider can handle several sequences of different types at once, and
can repeat the same analysis function on
several different sequences, resulting in multiple windows on the screen. To
obtain a copy of DNA Strider, send a formatted
800K disc and a self-addressed mailing label to:
Christian Marck,
Service de Biochimie,
Batiment 142, Centre d'Etudes Nucleaires de Saclay,
91191 Gif-sur-Yvette Cedex, FRANCE.