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. =============================================================================