Directory of MS DOS Molecular Biology Software on EMBL File Server
------------------------------------------------------------------
Version: 18-Apr-1991
To receive files from this directory use the command:
GET DOS_SOFTWARE:filename.ext
(a) Molecular Biology Software
filename ALX3.UAA
update 17-Nov-1989
version 1.0
size 140 k
compressed PAK
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Gotoh O.
description Alignment of three protein or DNA sequences
literatur J. Theor. Biol. 121 (1986), 327-337
source code -
sw requirements -
hw requirements -
filename BIGMOUTH.UAA
update 13-Feb-1990
version -
size 235 k
compressed PAK
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Jenson, H. B.
description Digitized sounds and utilities for TypeSeq and DigiSeq
literatur -
source code -
sw requirements DigiSeq or TypeSeq
hw requirements BigMouth sound digitizer
filename CIP.UUE
update 16-Jan-1990
version -
size 65 k
compressed PAK
ASCII conversion UUE
author Jenson, H. B.
description Calculation of reaction conditions for dephosphorylation
literatur -
source code -
sw requirements -
hw requirements -
filename CLONES.UAA
update 7-Mar-1990
version -
size 190 k
compressed PAK
ASCII conversion UUE (split; will be sent in 3 parts: .UAA to .UAC)
author Jenson, H. B.
description Management of clones, strains, libraries etc. databases
literatur BioTechniques 7 (1989), 590-592
source code -
sw requirements -
hw requirements -
filename CMOLECUL.UUE
update 6-Oct-1989
version May 87
size 70 k
compressed PAK
ASCII conversion UUE
author Thompson J. R. (Cedergren R.)
description graphics output of PCFOLD result files
literatur Nucl. Acids Res. 10 (1982), 8351-8356
source code available as MOLECSRC.UUE
sw requirements -
hw requirements CGA card
filename COSY.UAA
update 6-Nov-1990
version 4.0
size 1100 k
compressed PAK
ASCII conversion UUE (split; will be sent in 17 parts: .UAA to .UAQ)
author Eberhard M.
description Enzyme kinetics package
literature CABIOS 6 (1990), 213-221
source code Pascal
sw requirements -
hw requirements -
filename CREGEX.C
update 12-Jan-1991
version 1.1
size 10 k
compressed -
ASCII conversion -
author Leunissen J.
description Reformating of Prosite for use with Kolakowski's PROSEARCH
literature -
source code C
sw requirements (used by PROSEARCH [PROSEA12.UAA])
hw requirements -
filename CUTCOST.UUE
update 25-Sep-1990
version 2.1
size 95 k
compressed PAK
ASCII conversion UUE
author Meinhof C. G.
description Identification of cheapest source for restriction enzymes
literature -
source code -
sw requirements -
hw requirements -
filename DIGISEQ.UUE
update 13-Feb-1990
version -
size 80 k
compressed PAK
ASCII conversion UUE
author Jenson, H. B.
description Sequence input using digitizer
literatur CABIOS 4 (1988), 218
source code -
sw requirements -
hw requirements Graf/Bar 7 digitizing device
filename DNACLONE.UAA
update 16-Mar-1990
version 1.1
size 190 k
compressed PAK
ASCII conversion UUE (split; will be sent in 3 parts: .UAA to .UAC)
author Roy T. K.
description Management of clones, strains, libraries etc. databases
literatur CABIOS 5 (1989), 321-322
source code -
sw requirements -
hw requirements -
filename EASISTAT.UAA
update 15-Feb-1991
version 1.2
size 350 k
compressed PAK
ASCII conversion UUE (split; will be sent in 5 parts: .UAA to .UAE)
author Dave Curtis
description Package for statistical analyses
literature -
source code -
sw requirements -
hw requirements -
filename ELBAMAP.UUE
update 5-Jan-1990
version 2.2
size 55 k
compressed PAK
ASCII conversion UUE
author King G. J.
description Management of electrophoresis banding patterns
literatur CABIOS 5 (1989), 313-317
source code -
sw requirements -
hw requirements EGA card
filename EMOLECUL.UUE
update 6-Oct-1989
version May 87
size 70 k
compressed PAK
ASCII conversion UUE
author Thompson J. R. (Cedergren R.)
description graphics output of PCFOLD result files
literatur Nucl. Acids Res. 10 (1982), 8351-8356
source code available as MOLECSRC.UUE
sw requirements -
hw requirements EGA card
filename ENZKIN.UAA
update 16-Aug-1990
version 1.0
size 120 k
compressed PAK
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Maloy S. R.
description Enzyme kinetics calculation
literature CABIOS 6 (1990), 63-65
source code Fortran
sw requirements -
hw requirements Math co-processor
filename EPIPLOT.UAA
update 12-Jul-1990
version 1.0
size 128 k
compressed PAK
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Menendez-Arias L.
description Prediction of B and T cell epitopes from protein sequences
literatur CABIOS 6 (1990), 101-105
source code -
sw requirements -
hw requirements -
filename ESEE.UAA
update 25-Jun-1990
version 1.09d
size 180 k
compressed PAK
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author CABOT E.L.
description Multiple sequence editor
literatur CABIOS 5 (1989), 233-234
source code -
sw requirements -
hw requirements -
filename EZ-FIT.UAA
update 18-Oct-1989
version 1.1
size 170 k
compressed PAK
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Perella F. W.
description Calculation of enzyme and receptor kinetics
literatur Anal. Biochem. 174 (1989), 437-447
source code -
sw requirements -
hw requirements CGA card
filename FAST.UAA
update 26-Jan-1990
version -
size 195 k
compressed PAK
ASCII conversion UUE (split; will be sent in 3 parts: .UAA to .UAC)
author Facchiano, A.
description Protein structure analysis
literatur CABIOS 5 (1989), 299-303
source code -
sw requirements -
hw requirements CGA or EGA/VGA card
filename GEL.UUE
update 18-Oct-1989
version 17-Feb-1989
size 50 k
compressed PAK
ASCII conversion UUE
author Thompson J. R.
description Calculation of DNA restriction fragment sizes
literatur Anal. Biochem. 115 (81), 113-122
source code Pascal
sw requirements (Turbo Pascal for recompiling)
hw requirements -
filename HMOLECUL.UUE
update 6-Oct-1989
version May 87
size 70 k
compressed PAK
ASCII conversion UUE
author Thompson J. R. (Cedergren R.)
description graphics output of PCFOLD result files
literatur Nucl. Acids Res. 10 (1982), 8351-8356
source code available as MOLECSRC.UUE
sw requirements -
hw requirements Hercules card
filename HYDRASC.UUE
update 8-Oct-1989
version 1
size 30 k
compressed PAK
ASCII conversion UUE
author Penttila T. J.
description Contour map for two polypeptide sequences.
Regions with similar hydropathic properties and second.
structure properties are plotted.
literatur CABIOS, in prep.
source code -
sw requirements MATLAB-PC
hw requirements Math. co-processor, >2M RAM
filename LIGATE.UUE
update 16-Jan-1990
version -
size 75 k
compressed PAK
ASCII conversion UUE
author Jenson, H. B.
description Calculation of reaction conditions for ligation
literatur BioTechniques 5 (1987), 729-730
source code -
sw requirements -
hw requirements -
filename MARS.UAA
update 18-Jul-1990
version -
size 120 k
compressed PAK
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author De Boer, J. G.
description Finds sites in DNA which can easily be changed into
a restriction site by one or two changes
literatur CABIOS, submitted
source code -
sw requirements -
hw requirements -
filename MELPROT.UUE
update 27-Mar-1990
version -
size 80 k
compressed PAK
ASCII conversion UUE
author Sikaris K.
description Secondary structure prediction and plotting
literatur CABIOS 5 (1989), 323
source code Basic
sw requirements Any Basic interpreter
hw requirements -
filename MELT.UUE
update 25-May-1990
version 2.0
size 30 k
compressed PAK
ASCII conversion UUE
author Nash J.H.E.
description Melting point calculation of oligonucleotides
literatur -
source code -
sw requirements -
hw requirements -
filename MOLECSRC.UUE
update 6-Oct-1990
version May 87
size 70 k
compressed PAK
ASCII conversion UUE
author Thompson J. R. (Cedergren R.)
description Source code for *MOLECUL.UUE
literatur Nucl. Acids Res. 10 (1982), 8351-8356
source code Pascal
sw requirements Turbo Pascal
hw requirements -
filename MOTIF.UUE
update 8-Nov-1989
version - (bug fix with plain ASCII sequences)
size 45 k
compressed PAK
ASCII conversion UUE
author Giles I.
description Motif searching program
literatur CABIOS 5 (1989), 227-232
source code C
sw requirements (Turbo C for recompiling)
hw requirements -
filename MULTALIN.UAA
update 2-Apr-1990
version 3.0
size 130 k
compressed PAK
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Corpet F.
description Multiple sequence alignment
literatur Nucl. Acids Res. 16 (1988), 10881-10890
source code -
sw requirements -
hw requirements -
filename OLIGO.UAA
update 6-Oct-1989
version 1.0
size 105 k
compressed PAK
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Beadles K.
description Oligo-directed single amino acid substitution
literatur -
source code -
sw requirements -
hw requirements -
filename PATTERN.UUE
update 9-Nov-1989
version -
size 55 k
compressed PAK
ASCII conversion UUE
author Giles I.
description Pattern searching program
literatur CABIOS 5 (1989), 227-232
source code C
sw requirements (Turbo C for recompiling)
hw requirements -
filename PCFOLD.UAA
update 23-Oct-1989
version 4.0
size 160 k
compressed PAK
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Zuker M.
description RNA folding
literatur Meth. Enzymology 180 (1989), 262-288
source code Fortran, Asm
sw requirements (Compiler for recompiling)
hw requirements -
filename PEDRAW.UAA
update 15-Feb-1991
version ?
size 450 k
compressed PAK
ASCII conversion UUE (split; will be sent in 6 parts: .UAA to .UAF)
author Dave Curtis
description Pedigree drawing program
literature -
source code -
sw requirements -
hw requirements -
filename PLASMID.UUE
update 6-Oct-1989
version 1.1
size 75 k
compressed PAK
ASCII conversion UUE
author Lipsick J.
description Plasmid drawing program (CGA card req.)
literatur -
source code Basic
sw requirements (Quickbasic for recompiling)
hw requirements CGA card
filename PREDICT.UAA
update 20-Feb-1990
version 1.2
size 120 k
compressed PAK
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Carmenes R. S.
description Protein secondary structure predictions
literatur Biochem. Biophy. Res. Commun. 15 (1989), 687-698
source code -
sw requirements -
hw requirements -
filename PROGRAPH.UAA
update 18-Apr-1991
version 1.2
size 380 k
compressed PAK
ASCII conversion UUE (split; will be sent in 5 parts: .UAA to .UAE)
author Hoffmann K.
description Graphically oriented protein sequence analysis package
literature -
source code Pascal
sw requirements (Turbo Pascal for recompiling)
hw requirements Mouse
filename PRONET.UAA
update 23-Jan-1990
version 1.0
size 110 k
compressed PAK
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Pascarella S.
description Protein structure prediction with a neural network
literatur CABIOS 5 (1989), 319-320
source code Pascal
sw requirements (Turbo Pascal for recompiling)
hw requirements -
filename PROSEA12.UAA
update 24-Jan-1991
version 1.2
size 100 k
compressed PAK
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Kolakowski L. F.
description Pattern searching in proteins using Prosite
literature -
source code C
sw requirements Awk
hw requirements -
filename SDSE.UAA
update 24-Nov-1989
version 2.0
size 185 k
compressed PAK
ASCII conversion UUE (split; will be sent in 3 parts: .UAA to .UAC)
author Oliver J. L.
description Simulation of DNA sequence evolution
literatur CABIOS 5 (1989), 47-50
source code -
sw requirements -
hw requirements -
filename SEQAIDFD.UAA
update 25-Sep-1990
version 3.8
size 300 k
compressed PAK
ASCII conversion UUE (split; will be sent in 3 parts: .UAA to .UAC)
author Roufa D.
description DNA and protein sequence analysis package
literatur -
source code -
sw requirements -
hw requirements -
filename SIGSEQ.UUE
update 11-Dec-1989
version 1.0
size 60 k
compressed PAK
ASCII conversion UUE
author Popowicz A.M.
description Prediction of signal sequence cleavage site
literatur CABIOS 4 (1988), 405-406
source code C
sw requirements (Compiler for recompiling)
hw requirements -
filename SIM.UUE
update 12-Feb-1991
version -
size 30 k
compressed PAK
ASCII conversion UUE
author Huang G. and Miller W.
description Local similarity searching
literature CABIOS 6 (1990), 373 - 381.
source code C
sw requirements -
hw requirements -
filename SUBSIS.UUE
update 18-May-1990
version 1.2
size 15 k
compressed PAK
ASCII conversion UUE
author Mandler J.
description Subdirectory handling with DNASIS(tm) or PROSIS(tm)
literature CABIOS 6 (1990), 291-292
source code GWBASIC
sw requirements GWBASIC, DNASIS or PROSIS, MS-DOS DEBUG
hw requirements -
filename TDALIGN.UAA
update 18-Nov-1989
version 1.61
size 120 k
compressed PAK
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Davison D. (Thompson K.)
description Sequence alignment
literatur -
source code -
sw requirements -
hw requirements -
filename TFD2PROSITE.C
update 25-Feb-1991
version 1.1
size 10 k
compressed -
ASCII conversion -
author Fuchs R.
description Program to convert SITES and DOMAINS tables of TFD
database to Prosite format.
literature -
source code C
sw requirements -
hw requirements -
filename TYPESEQ.UUE
update 13-Feb-1990
version -
size 55 k
compressed PAK
ASCII conversion UUE
author Jenson, H. B.
description Sequence input using keyboard
literatur CABIOS 4 (1988), 218
source code -
sw requirements -
hw requirements -
(b) Archiving/Decoding Software
filename UUEMBL.UUE
update 6-Feb-1991
version -
size 60 k
compressed PAK
ASCII conversion UUE
author Fuchs R. (Dumas M.)
description UUEncoded form of UUD uudecoder and UUE uuencoder
literatur -
source code C
sw requirements -
hw requirements -
filename UUD.C
update 6-Feb-1991
version -
size 20 k
compressed no
ASCII conversion no
author Dumas M.
description Source code for recommended uudecoder
literatur -
source code C
sw requirements Turbo C
hw requirements -
filename UUDECODE.PAS
update 4-Dec-1989
version 4-Dec-1989
size 6 k
compressed no
ASCII conversion no
author -
description Source code for bootstrap uudecoder
literatur -
source code Pascal
sw requirements Turbo Pascal
hw requirements -
filename UUD19.BAS
update 6-Oct-1989
version -
size 5 k
compressed no
ASCII conversion no
author -
description Source code for bootstrap uudecoder
literatur -
source code Basic
sw requirements GWBasic
hw requirements -
filename DETAR.UUE
update 2-Mar-1990
version -
size 45 k
compressed PAK
ASCII conversion UUE
author VALVERDE J. R.
description Utility to extract .TAR files
literatur -
source code C
sw requirements Turbo C (for recompiling)
hw requirements -
filename PRNTGL.UUE
update 10-Oct-1990
version 1.09
size 120 k
compressed PAK
ASCII conversion UUE
author Ravitz, C.
description Prints HGPL files (like produced by GCG) on matrix or
laser printer
literatur -
source code -
sw requirements -
hw requirements -
Files with the extension ".uue", ".uaa" etc. must be decoded with UUD.
=============================================================================
Directory of Apple Macintosh Molecular Biology Software on EMBL File Server
---------------------------------------------------------------------------
Version: 29-Apr-1991
To receive files from this directory use the command:
GET MAC_SOFTWARE:filename.ext
(a) Molecular Biology Software
filename BUFSTACK.HQX
update 17-Nov-1989
version 1.1
size 80 k
compressed StuffIt
ASCII conversion StuffIt
author Beynon R. J.
description Calculation of thermodynamically-corrected buffer recipes
literature CABIOS 4 (1988), 487-490
source code -
sw requirements HyperCard
hw requirements -
filename CGR.HQX
update 10-Aug-1990
version 1.0
size 40 k
compressed StuffIt
ASCII conversion StuffIt
author Lehvaslaiho H.
description Chaos game representation of DNA sequences
literature -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename DNAID.HQX
update 19-Oct-1989
version 1.1
size 230 k
compressed StuffIt
ASCII conversion StuffIt
author Dardel F.
description DNA sequence editor with grep-like search routine
literature CABIOS 4 (1988), 483-486
source code -
sw requirements -
hw requirements -
filename DNATRANSLATOR.HQX
update 4-Apr-1991
version 0.98.1
size 400 k
compressed Compactor (self-extracting)
ASCII conversion BinHex
author Eernisse D. J.
description HyperCard stack with utilities for phylogenetic analyses
literature -
source code HyperTalk
sw requirements HyperCard 2.0
hw requirements -
filename DOTTYPLOT.HQX
update 20-Nov-1989
version 1.0c
size 210 k
compressed StuffIt
ASCII conversion StuffIt
author Gilbert D.
description Dot-matrix comparison of DNA sequences
literature CABIOS 6 (1990), 117
source code Pascal source for sequence loading subroutine
sw requirements -
hw requirements -
filename EMBL-SEARCH.HQX
update 15-Apr-1991
version 1.0
size 140 k
compressed Compactor (self-extracting)
ASCII conversion BinHex
author Fuchs R.
description Entry retrieval from EMBL CD-ROM
literature -
source code Think C
sw requirements -
hw requirements EMBL CD-ROM
filename ENDOCYTOSIS.HQX
update 8-Nov-1990
version 0.1
size 150 k
compressed StuffIt
ASCII conversion StuffIt
author Williams R.E.
description Calculation of parameters of endocytosis reaction
literature -
source code -
sw requirements -
hw requirements -
filename ENZYMEKIN.HQX
update 22-Sep-1989
version 1.0
size 105 k
compressed StuffIt
ASCII conversion StuffIt
author Gilbert D.
description Calculation of enzyme kinetics
literature CABIOS 6 (1990), 113-116
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename GELFRAG.HQX
update 22-Sep-1989
version 1.4
size 145 k
compressed StuffIt
ASCII conversion StuffIt
author Gilbert D.
description Calculation of DNA restriction fragment sizes
literature CABIOS 6 (1990), 113-116
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename LOOPVIEWER.HQX
update 6-Nov-1990
version 1.0
size 150 k
compressed StuffIt
ASCII conversion StuffIt
author Gilbert D.
description Graphical representation of RNA folding
literature -
source code -
sw requirements (MulFold is optional)
hw requirements -
filename MACCLADE.HQX
update 20-Mar-1990
version 2.1
size 140 k
compressed StuffIt
ASCII conversion StuffIt
author Maddison W and Maddison D
description Phylogeny program
literature -
source code -
sw requirements -
filename MACDNA.HQX
update 24-Nov-1989
version 2/88
size 65 k
compressed StuffIt
ASCII conversion StuffIt
author Schleif R.
description DNA sequence analysis, ported from IBM-PC
literature -
source code -
sw requirements -
filename MACLIGAND.HQX
update 6-Nov-1990
version 1.02
size 115 k
compressed StuffIt
ASCII conversion StuffIt
author Williams R.E.
description Calculation of parameters of ligand binding
literature -
source code -
sw requirements -
hw requirements -
filename MACMOLECULE.HQX
update 17-Dec-1990
version 1.0
size 410 k
compressed StuffIt
ASCII conversion StuffIt
author Myers E., Blanco C., Hallick R.B. and Jahnke J.
description 3D models of biomolecules
literature -
source code -
sw requirements -
hw requirements -
filename MACPATTERN.HQX
update 3-Apr-1991
version 1.2.5
size 180 k
compressed Compactor (self-extracting)
ASCII conversion BinHex
author Fuchs R.
description Pattern searching in conjunction with Prosite database
literature -
source code -
sw requirements Prosite pattern database
hw requirements -
filename MACPLASMAP.HQX
update 28-Mar-1990
version 1.82
size 270 k
compressed Compactor (self-extracting)
ASCII conversion BinHex
author Liu J.
description Plasmid drawing program.
literature -
source code -
sw requirements -
filename MACTARGSEARCH.HQX
update 29-Apr-1991
version 2.0
size 110 k
compressed StuffIt
ASCII conversion StuffIt
author Goodrich J.A., McClure W.R., and Schwartz M.L.
description DNA profile searching
literature -
source code Basic
sw requirements -
hw requirements -
filename MATMETH.HQX
update 4-Mar-1991
version 5.0
size 150k
compressed Compactor (self-extracting)
ASCII conversion BinHex
author Brown J.
description Molecular biological protocols
literature -
source code HyperTalk
sw requirements HyperCard 2.0
hw requirements -
filename MINIMM.HQX
update 16-Jan-1990
version 4.0
size 210 k
compressed StuffIt
ASCII conversion StuffIt
author Brown J.
description Molecular biological protocols (more HyperCard-like)
literature -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename MULFOLD.HQX
update 6-Nov-1990
version 2.0
size 282 k
compressed StuffIt
ASCII conversion StuffIt
author Zuker M.
description Calculation of RNA folding
literature Science 244 (1989), 48-52
source code -
sw requirements -
hw requirements -
filename READSEQ.HQX
update 3-Apr-1990
version -
size 70 k
compressed StuffIt
ASCII conversion StuffIt
author Gilbert D.
description Pascal and C routines for handling different sequence
file formats (EMBL,IG,Strider etc.)
literature -
source code Pascal, C
sw requirements Pascal or C compiler
hw requirements -
filename REFSTACK.HQX
update 16-Jan-1990
version 2.0
size 145 k
compressed StuffIt
ASCII conversion StuffIt
author Brown J.
description Management of literature references
literature -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename RIMANAGER.HQX
update 6-Dec-1990
version 1.67
size 420 k
compressed StuffIt
ASCII conversion StuffIt
author Manly K.
description Analysis of genetic mapping experiments with
recombinant mouse strains.
literature -
source code -
sw requirements -
hw requirements -
filename RRNA1.HQX
update 30-Oct-1989
version 0.3
size 165 k
compressed StuffIt
ASCII conversion StuffIt
author Brown J.
description Phylogeny of 16/18S rRNA (part 1 of 2)
literature -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename RRNA2.HQX
update 30-Oct-1989
version 0.3
size 120 k
compressed StuffIt
ASCII conversion StuffIt
author Brown J.
description Phylogeny of 16/18S rRNA (part 2 of 2)
literature -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename SEQLOGO.HQX
update 4-Feb-1991
version ?
size 500 k
compressed Compactor (self-extracting)
ASCII conversion BinHex
author Schneider T.
description Displaying consensus sequences by means of 'logos'
literature Nucl. Acids Res. 18 (1990), 6097-6100
source code Pascal
sw requirements -
hw requirements -
filename SPEAKQUENCER.HQX
update 6-Nov-1990
version 1.1.1
size 100 k
compressed StuffIt
ASCII conversion StuffIt
author Fritze C.
description Sequence data entry with acoustic feedback
literature -
source code -
sw requirements -
hw requirements -
filename TFD2PROSITE.C
update 25-Feb-1991
version 1.1
size 10 k
compressed -
ASCII conversion -
author Fuchs R.
description Program to convert SITES and DOMAINS tables of TFD
database to Prosite format.
literature -
source code C
sw requirements -
hw requirements -
filename THREE.HQX
update 29-Sep-1989
version -
size 80 k
compressed StuffIt
ASCII conversion StuffIt
author Markiewicz P. (Johnson M.)
description Alignment of three protein sequences
literature -
source code -
sw requirements -
hw requirements -
filename TREEDRAW.HQX
update 26-Jun-1990
version -
size 180 k
compressed StuffIt
ASCII conversion StuffIt
author Gilbert D.
description Drawing of phylogenetic trees
literature -
source code Pascal, C, HyperTalk
sw requirements HyperCard
hw requirements -
filename TRNA-SEARCH.HQX
update 10-Apr-1991
version 1.0
size 200 k
compressed Compactor (self-extracting)
ASCII conversion BinHex
author Shortridge R. D. (Markiewicz P.)
description Identification of tRNA genes and plotting of RNA structure
literature CABIOS 2 (1986), 13-17
source code -
sw requirements -
hw requirements -
(b) Decoding software
filename STUFFIT_16.HQX
update 8-Oct-1990
version 1.6
size 500 k
compressed -
ASCII conversion StuffIt
author Lau R.
description Installer for latest version of StuffIt Classic
literature -
source code -
sw requirements -
hw requirements -
filename UNSTUFFITDELUXE.HQX
update 8-Jan-1991
version 2.0
size 180 k
compressed -
ASCII conversion StuffIt
author Lau R.
description Installer for UnStuffIt Deluxe
literature -
source code -
sw requirements -
hw requirements -
filename UUD.C
update 2-Apr-1991
version -
size 20 k
compressed no
ASCII conversion no
author Dumas M.
description C source code for UUD uudecoder
literature -
source code C
sw requirements -
hw requirements -
filename UUD.HQX
update 2-Apr-1991
version -
size 50 k
compressed Compactor (self-extracting)
ASCII conversion BinHex
author Dumas M.
description C source code for UUD uudecoder
literature -
source code C
sw requirements -
hw requirements -
(c) Other
MACREVIEW.1 - Peter Markiewicz's reviews of molecular biology software
MACREVIEW.2 available for the Macintosh (Feb. 1991)
Files with the extension ".hqx" have to be decoded by (Un)StuffIt.
=============================================================================
Directory of UNIX Molecular Biology Software on EMBL File Server
---------------------------------------------------------------
Version: 3-Apr-1991
To receive files from this directory use the command:
GET UNIX_SOFTWARE:filename.ext
(a) Molecular Biology Software
filename BLAST.UAA
update 26-Oct-1990
version -
size 200 k
compressed TAR, COMPRESS
ASCII conversion UUE (split; will be sent in 3 parts: .UAA to .UAC)
author Myers E.W., Miller W., Altschul S.F., Gish W. and
Lipman, D.J.
description Fast sequence database searching.
literature J. Mol. Biol. 215 (1990), 403-410
source code C
sw requirements Files DFA and LIBNCBI are required!
hw requirements -
filename CREGEX.C
update 12-Jan-1991
version 1.1
size 10 k
compressed -
ASCII conversion -
author Leunissen J.
description Reformating of Prosite for use with Kolakowski's PROSEARCH
literature -
source code C
sw requirements (used by PROSEARCH [PROSEARCH.UAA])
hw requirements -
filename DFA.UAA
update 12-Nov-1990
version -
size 125 k
compressed TAR, COMPRESS
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Gish W.
description Routines for finite state automaton used by BLAST
literature J. Mol. Biol. 215 (1990), 403-410
source code C
sw requirements -
hw requirements -
filename GM.UAA
update 23-Jul-1990
version -
size 360 k
compressed TAR, COMPRESS
ASCII conversion UUE (split; will be sent in 4 parts: .UAA to .UAD)
author Fields C.A. and Soderlund C.A.
description Analysis of unknown DNA sequences
literature CABIOS 6 (1990), 263-270
source code C
sw requirements -
hw requirements -
filename HOMOCHART.UUE
update 3-Apr-1991
version -
size 20 k
compressed TAR, COMPRESS
ASCII conversion UUE
author Smith R.
description Plotting multiple sequence alignments with boxes around
identical residues
literature -
source code C
sw requirements -
hw requirements -
filename LIBNCBI.UAA
update 26-Oct-1990
version -
size 115 k
compressed TAR, COMPRESS
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Gish W.
description General purpose routines used by BLAST
literature J. Mol. Biol. 215 (1990), 403-410
source code C
sw requirements -
hw requirements -
filename MASE.UAA
update 30-Jul-1990
version -
size 930 k
compressed TAR, COMPRESS
ASCII conversion UUE (split; will be sent in 11 parts: .UAA to .UAK)
author Faulkner D. V.
description Multiple sequence editor
literatur TIBS 13 (1989), 321-322
source code C
sw requirements -
hw requirements -
filename MFASTA.UUE
update 31-Jul-1990
version 1.2
size 21 k
compressed -
ASCII conversion UUE
author deBoer T.
description Script for using EMBL/GenBank Mail-FASTA servers
literatur -
source code C
sw requirements -
hw requirements -
filename PLSEARCH.UAA
update 21-Aug-1990
version 4.0
size 2550 k
compressed TAR, COMPRESS
ASCII conversion UUE (split; will be sent in 30 parts: .UAA to .UBD)
author Smith, R.F. and Smith T.F.
description Pattern detection in proteins
literatur -
source code C
sw requirements -
hw requirements -
filename PROSEARCH.UAA
update 24-Jan-1991
version 1.2
size 85 k
compressed TAR, COMPRESS
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Kolakowski L. F.
description Pattern searching in proteins using Prosite (incl.
CREGEX.C and TFD2PROSITE.C)
literatur -
source code C
sw requirements Awk
hw requirements -
filename SEQF.UAA
update 12-Feb-1991
version -
size 140 k
compressed TAR, COMPRESS
ASCII conversion UUE (split; will be sent in 3 parts: .UAA to .UAC)
author Davison D. and Kanehisa M.
description Package of programs for searching genetic sequence
libraries.
literature -
source code C
sw requirements -
hw requirements -
filename SIGSEQ.UUE
update 19-Jul-1990
version -
size 20 k
compressed TAR, COMPRESS
ASCII conversion UUE
author Popowicz A.M.
description Prediction of signal sequence cleavage site
literatur CABIOS 4 (1988), 405-406
source code C
sw requirements -
hw requirements -
filename SIM.UUE
update 7-Nov-1990
version -
size 30 k
compressed TAR, COMPRESS
ASCII conversion UUE
author Huang G. and Miller W.
description Local similarity searching
literature CABIOS 6 (1990), 373 - 381.
source code C
sw requirements -
hw requirements -
filename TFD2PROSITE.C
update 25-Feb-1991
version 1.1
size 10 k
compressed -
ASCII conversion -
author Fuchs R.
description Program to convert SITES table of TFD database to
Prosite format.
literature -
source code C
sw requirements -
hw requirements -
filename TREEALIG.UAA
update 23-Nov-1990
version Nov 1990
size 300 k
compressed TAR, COMPRESS
ASCII conversion UUE (split; will be sent in 4 parts: .UAA to .UAD)
author Hein J.
description Multiple sequence alignment and phylogeny
literature Meth. Enzymol. 183 (1990), 626-644
source code C
sw requirements -
hw requirements -
(b) Decoding Software
filename UUD.C
update 2-Apr-1991
version -
size 20 k
compressed no
ASCII conversion no
author Dumas M.
description C source code for UUD uudecoder
literatur -
source code C
sw requirements -
hw requirements -
filename UUE.C
update 20-Jul-1990
version -
size 6 k
compressed no
ASCII conversion no
author Dumas M.
description C source code for UUE uuencoder
literatur -
source code C
sw requirements -
hw requirements -
Files with the extension ".uue", ".uaa" etc. must be decoded by UUD.
=============================================================================
Directory of VAX Molecular Biology Software on EMBL File Server
---------------------------------------------------------------
Version: 10-Apr-1991
To receive files from this directory use the command:
GET VAX_SOFTWARE:filename.ext
(a) Molecular Biology Software
filename AMPHI.UUE
update 12-Apr-1990
version -
size 30 k
compressed ZOO
ASCII conversion UUE
author Jaehnig F.
description Prediction of membran protein structure
literature Trends in Biochemistry 3 (1990)
source code Fortran
sw requirements GCG v6 for plotting (works without GCG)
hw requirements -
filename BOXSHADE.UUE
update 10-Apr-1991
version 1.0
size 30 k
compressed ZOO
ASCII conversion UUE
author Hoffmann K.
description Plots multiple alignments, marking identical or
similar residues
literature -
source code Pascal
sw requirements UIS software
hw requirements VAXstations or LJ250 color printer
filename BUGFIX_6_1.GCG
update 18-Dec-1989
version -
size 9 k
compressed -
ASCII conversion -
author -
description Fixes for several bugs in GCG package v6.1
literature -
source code -
sw requirements GCG package,Fortran compiler, C compiler
hw requirements -
filename CKIT.UAA
update 2-Aug-1990
version 2.1
size 245 k
compressed ZOO
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Gilbert W.A.
description C toolbox for writing sequence analysis programs
literature -
source code -
sw requirements VAX C compiler
hw requirements -
filename CLUSTAL.UUE
update 15-Mar-1990
version -
size 50 k
compressed ZOO
ASCII conversion UUE
author Higgins D.
description Multiple sequence alignment
literature Gene 73 (198), 237-244
source code -
sw requirements -
hw requirements -
filename CREGEX.C
update 12-Jan-1991
version 1.1
size 10 k
compressed -
ASCII conversion -
author Leunissen J.
description Reformating of Prosite for use with Kolakowski's PROSEARCH
literature -
source code C
sw requirements (used by PROSEARCH [PROSEARCH.UAA])
hw requirements -
filename FASTEMBL.COM
update 5-Dec-1990
version 1.1
size 15k
compressed ZOO
ASCII conversion UUE
author Sonnhammer E. L. (Clark S.)
description DCL shell for facilitating EMBL Mail-FASTA access
literature -
source code DCL
sw requirements -
hw requirements -
filename GCGDBASE.UAA
update 23-Mar-1990
version -
size 120 k
compressed ZOO (split; will be sent in 2 parts: .UAA and .UAB)
ASCII conversion UUE
author Rice P.
description GCG extensions developed at EMBL for using new EMBL
distribution format
literature -
source code Fortran
sw requirements GCG package v6
hw requirements -
filename GCGEMBL.UAA
update 30-Oct-1989
version -
size 180 k
compressed ZOO (split; will be sent in 4 parts: .UAA to .UAD)
ASCII conversion UUE
author Rice P.
description GCG extensions developed at EMBL
literature -
source code Fortran
sw requirements GCG package v5 or v6
hw requirements -
filename GCGQUICK.UAA
update 25-Apr-1990
version -
size 150 k
compressed ZOO (split; will be sent in 2 parts: .UAA and .UAB)
ASCII conversion UUE
author Rice P.
description GCG extensions developed at EMBL for speeding up
QuickSearch
literature -
source code Fortran
sw requirements GCG package v6
hw requirements -
filename GCGSHELLS1.TXT
update 7-May-1990
version May 1990
size 90 k
compressed -
ASCII conversion -
author Clark S.
description DCL shells for many GCG programs
literature -
source code DCL, Fortran
sw requirements VAX Fortran
hw requirements -
filename GCGSHELLS2.TXT
update 13-Mar-1990
version -
size 90 k
compressed -
ASCII conversion -
author Clark S.
description DCL shells to facilitate GenBank on-line service access
literature -
source code DCL, Fortran
sw requirements VAX Fortran
hw requirements -
filename MOTIF.UUE
update 9-Nov-1989
version -
size 90 k
compressed ZOO
ASCII conversion UUE
author Giles I.
description Motif searching program
literature CABIOS 5 (1989), 227-232
source code C
sw requirements VAX C for recompiling
hw requirements -
filename MSE.UUE
update 2-Aug-1990
version 2.0
size 90 k
compressed ZOO
ASCII conversion UUE
author Gilbert W.A.
description Multiple sequence editor
literature -
source code -
sw requirements -
hw requirements -
filename NOCUT.COM
update 21-Aug-1990
version 21-Aug-1990
size 12 k
compressed -
ASCII conversion -
author Easton T.
description Production of restriction enzyme database file of
non-cutters taken from MAP output for use with MAP/SIL.
literature -
source code DCL
sw requirements GCG
hw requirements -
filename PATTERN.UAA
update 9-Nov-1989
version -
size 100 k
compressed ZOO (split; will be sent in 2 parts: .UAA and .UAB)
ASCII conversion UUE
author Giles I.
description Pattern searching program
literature CABIOS 5 (1989), 227-232
source code C
sw requirements VAX C for recompiling
hw requirements -
filename PROFILESCAN.BUGFIX
update 7-Sep-1990
version -
size 4 k
compressed -
ASCII conversion -
author Gribskov M.
description Bug fix for the GCG program PROFILESCAN
literature -
source code -
sw requirements GCG package,Fortran compiler
hw requirements -
filename PROINDEX.UUE
update 1-Jun-1990
version -
size 45 k
compressed -
ASCII conversion -
author Clark S.
description Index file creation for ProSite pattern database
literature -
source code Fortran
sw requirements VAX Fortran
hw requirements -
filename PROSEARCH.UAA
update 24-Jan-1991
version 1.2
size 80 k
compressed ZOO
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Kolakowski L. F.
description Pattern searching in proteins using Prosite (incl.
CREGEX.C and TFD2PROSITE.C)
literature -
source code C
sw requirements Awk
hw requirements -
filename PROSITEC.UUE
update 7-Jun-1990
version 1.1
size 40 k
compressed ZOO
ASCII conversion UUE
author Hofmann K.
description Conversion of Prosite database to GCG Find format
literature -
source code Pascal
sw requirements VAX Pascal for recompiling
hw requirements -
filename READSEQ.UUE
update 25-Jul-1990
version July 1990
size 75 k
compressed ZOO
ASCII conversion UUE
author Gilbert D.
description Multiple sequence format conversion program
literature -
source code C
sw requirements VAX C for recompiling
hw requirements -
filename RST_OLAP.UUE
update 5-Oct-1990
version 1.0
size 45 k
compressed ZOO
ASCII conversion UUE
author Stockwell P. A.
description Creates sorted list of restrictione enzymes giving
adhesive ends from REBASE database file
literature -
source code Pascal
sw requirements -
hw requirements -
filename SCRUTINE.UAA
update 11-Mar-1991
version 2.?
size 720 k
compressed ZOO
ASCII conversion UUE (split; will be sent in 12 parts: .UAA to .UAL)
author Sibbald P.
description SCRUTINEER: a package for searching protein sequence
databases
literature CABIOS 6 (1990), 279-288
source code Pascal
sw requirements VAX Pascal for recompiling
hw requirements -
filename SEQEDT.UUE
update 2-Aug-1990
version 2.0
size 80 k
compressed ZOO
ASCII conversion UUE
author Gilbert W.A.
description Sequence editor, modelled on EDT
literature -
source code -
sw requirements -
hw requirements -
filename SIM.UUE
update 12-Feb-1991
version -
size 30 k
compressed ZOO
ASCII conversion UUE
author Huang G. and Miller W.
description Local similarity searching
literature CABIOS 6 (1990), 373 - 381.
source code C
sw requirements -
hw requirements -
filename STATSRCH.UAA
update 18-May-1990
version -
size 145 k
compressed ZOO (split; will be sent in 2 parts: .UAA and .UAB)
ASCII conversion UUE
author Mott R. F.
description Database searching taking into account the statistical
significance of any similarities found
literature CABIOS, 6 (1990), 293-295
source code Fortran
sw requirements GCG package
hw requirements -
filename TFD2PROSITE.C
update 25-Feb-1991
version 1.1
size 10 k
compressed -
ASCII conversion -
author Fuchs R.
description Program to convert SITES and DOMAINS tables of TFD
database to Prosite format.
literature -
source code C
sw requirements -
hw requirements -
filename TREEALIG.UAA
update 23-Nov-1990
version Nov 1990
size 300 k
compressed ZOO
ASCII conversion UUE (split; will be sent in 4 parts: .UAA to .UAD)
author Hein J.
description Multiple sequence alignment and phylogeny
literature Meth. Enzymol. 183 (1990), 626-644
source code C
sw requirements VAX C for recompiling
hw requirements -
(b) Decoding Software
filename OLDZOO.UUE
update 27-Jun-1990
version 1.6 (1-Aug-1987)
size 55 k
compressed no
ASCII conversion UUE
author Dhesi R.
description Archiving program
literature -
source code -
sw requirements -
hw requirements -
filename UUD.C
update 2-Apr-1991
version -
size 20 k
compressed no
ASCII conversion no
author Dumas M.
description C source code for UUD uudecoder
literature -
source code C
sw requirements VAX C
hw requirements -
filename UUE.C
update 25-Sep-1989
version -
size 6 k
compressed no
ASCII conversion no
author Dumas M.
description C source code for UUE uuencoder
literature -
source code C
sw requirements VAX C
hw requirements -
filename ZOO.UAA
update 27-Sep-1990
version 2.01 (25-Aug-1988)
size 90 k
compressed no
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Dhesi R.
description Archiving program
literature -
source code -
sw requirements -
hw requirements -
(c) Other software
filename CDACCESS.UAA
update Feb-1991
version 2.05
size 180 k
compressed ZOO
ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB)
author Stockwell P.A.
description Driver software for ISO-formatted CD-ROMs
literature -
source code Pascal
sw requirements VAX Pascal
hw requirements CD-ROM drive
Files with the extension ".uue", ".uaa" et. must be decoded by UUD. The
resulting ZOO-archives have to be extracted by ZOO.
=============================================================================