Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00010 NAME BLAST-SHELL DOMAIN Alignment Search software DOMAIN GCG tools DESCRIPTION These programs construct messages in the DESCRIPTION format expected by GenBank and send them by DESCRIPTION mail. The users do not have to be familiar DESCRIPTION with the format of the message that GenBank DESCRIPTION expects,nor with sending email across the DESCRIPTION network; however, they do need to know how to DESCRIPTION read the mail that GenBank returns. DESCRIPTION BLASTMAIL.COM initiates a BLAST search of one DESCRIPTION of the GenBank databases. DESCRIPTION BLASTMAILQ.COM sends a message to the GenBank DESCRIPTION BLAST server inquiring about the state of the DESCRIPTION queue. TOFASTA.FOR is a program that converts DESCRIPTION a GCG sequence to the Fasta format expected DESCRIPTION by the GenBank server. AUTHOR Stephen Clark RT - ADDRESS U. of Virginia Dept. of Biochemistry, USA CONTACT clark@galen.oci.utoronto.ca (Internet) SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/vax SITE-CONTACT D Gilbert: gilbertd@cricket.bio.indiana.edu OS VAX/VMS LANGUAGE - VOLUME - REQUIRES This program will have to be compiled REQUIRES and linked under the GCG environment. AC BC00105 NAME INTERFACE DOMAIN GCG tools DESCRIPTION provides the needed interface to write Pascal DESCRIPTION programs using the Genetics Computer Group's DESCRIPTION Device-Independent Graphic Primitives DESCRIPTION Procedure Library. The implementation of DESCRIPTION interfaces for the other subroutines DESCRIPTION in the GCG library can be infered from this DESCRIPTION example.The original PlotTest.For program DESCRIPTION provided with the GCG package is included, in DESCRIPTION a loose Pascal translation, as an example on DESCRIPTION how to use the interface AUTHOR Prilusky J. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS VAX/VMS LANGUAGE Pascal C VOLUME - REQUIRES GCG for linking the Procedure Library AC BC00106 NAME MOBILITY DOMAIN GCG tools DESCRIPTION This is a modification of the GCG Peptidesort program to caclulate the DESCRIPTION gel mobility of peptide fragments under different conditions. DESCRIPTION Mobility and Peptidesort are written with the GCG procedure library and use DESCRIPTION GCG file formats and interface. Peptidesort is a modification of the GCG program DESCRIPTION Peptidesort. It calculates two more values, the electrophoretic mobility and DESCRIPTION the chromatographic mobility (these two values are plotted by Mobility), and DESCRIPTION prompts for a buffer and pH level. It also lists the sequence of each peptide. DESCRIPTION The output file from Peptidesort is used as the input to Mobility. Mobility is DESCRIPTION simply a plotting program. DESCRIPTION Peptidesort has a few command line switches which most people will want to use. DESCRIPTION /CYSTEICACID DESCRIPTION Converts cysteine residues to cysteic acid DESCRIPTION /PHOSphorylated=23 DESCRIPTION Marks the residue at the specified position as phosphorylated. DESCRIPTION /DONTCut=2,5,14,20 DESCRIPTION Prevents enzymes from cutting after selected residues. DESCRIPTION /SELECT=C DESCRIPTION Only prints those peptides which contain the specified amino acid. DESCRIPTION Mobility reads the Peptidesort output file and prompts you for the numbers of DESCRIPTION the peptides you want to plot. Peptides which contain phosphorylated residues DESCRIPTION are marked by diamonds. AUTHOR - ADDRESS - CONTACT - SITE ftp anonymous axp1.salk.edu SITE Directory /mobility SITE-CONTACT - OS VMS (executables provided) LANGUAGE FORTRAN VOLUME - REQUIRES - COMMENTS The methods used in this program are described in COMMENTS Methods of Enz, Acad Press, v.200,201, 1991. AC BC00107 NAME PROFILEWEIGHT DOMAIN GCG tools DESCRIPTION Creation of sequence profiles for use with GCG DESCRIPTION ProfileSearch AUTHOR Thompson J. RA Thompson J.D., Higgins D.G., Gibson T.J.; RT "Improved sensitivity of profile searches through the use of sequence RT weights and gap excision."; RL Comput. Appl. Biosci. 10:19-29(1994). RX Medline; 94251642. RX SeqAnalRef; THOD9401. ADDRESS European Molecular Biology Laboratory, Heidelberg, Germany. CONTACT Gibson@EMBL-Heiddelberg.DE SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk OS Unix, VAX/VMS LANGUAGE C VOLUME - AC BC00108 NAME SCUO DOMAIN GCG tools DESCRIPTION The SCUO software is based on the development of an information DESCRIPTION theory based index for characterizing synonymous codon usage bias DESCRIPTION without requiring a reference set of sequences.This index provide DESCRIPTION a way to quantify the "orderliness" of synonymous codon usage and DESCRIPTION the severity of the constraints towards non-random synonymous DESCRIPTION codon usage. The software may prove useful in predicting the DESCRIPTION relative level of gene expression, for making comparisons of DESCRIPTION the degree of synonymous codon usage bias in different DESCRIPTION organisms, for finding protein coding regions in sequenced DESCRIPTION DNA, for distinguishing between exons and introns and for DESCRIPTION detecting frame shift sequencing errors. AUTHOR Jizhong Zhou,Michael E. Moody, Susan Jean Johns, Andris Kleinhofs RA Zhou J., Moody M.E., Johns S.J., Kleinhofs A.; RT "An Informational Index for Measuring Codon Usage Bias."; ADDRESS - CONTACT prcadams@jaguar.csc.wsu.edu (Susan Jean Johns) SITE ftp anonymous bobcat.csc.wsu.edu SITE Directory /molbio/scuo SITE-CONTACT prcadams@jaguar.csc.wsu.edu OS Vax/VMS, UNIX LANGUAGE FORTRAN VOLUME - REQUIRES GCG libraries COMMENTS Initially built on VMS using GCG6.0 libraries. COMMENTS Has been built successfully with GCG7.0 on SUNos4.1x. AC BC00134 NAME MidasPlus DOMAIN Molecular modelling and graphics DESCRIPTION Molecular Interactive Display and Simulation DESCRIPTION proteins, nucleic acids, drugs DESCRIPTION Input_Format: PDB DESCRIPTION Output_Format: PDB DESCRIPTION Molecular_Model: wire, stick, stick_and_ball, CPK, ribbon DESCRIPTION Output_Type: display, PostScript, SGI "Image File" AUTHOR T.E. Ferrin, C.C. Huang, L.E. Jarvis and R. Langridge RA Ferrin T.E., Huang C.C., Jarvis L.E., Langridge R.; RT "The MIDAS display system"; RL J. Mol. Graph. 6(1):13-27(1988). RA Huang C.C., Pettersen E.F., Klein T.E, Ferrin T.E., Langridge R.; RT "Conic: A fast renderer for space-filling molecules with shadows."; RT J. Mol. Graph. 9(4):230-236(1991). RX Medline; 92126623. RA Ferrin T.E., CouchG.S., Huang C.C., Pettersen E.F., Langridge R.; RT "An Affordable Approach to Interactive Desktop Molecular Modeling"; RL J. Mol. Graph. 9(1):27-32,37-38(1991). ADDRESS Computer Graphics Laboratory ADDRESS University of California, San Francisco ADDRESS Tel: +1-415-476-5128 ADDRESS Fax: +1-415-476-0866 CONTACT midasplus@cgl.ucsf.edu SITE - SITE-CONTACT - OS Unix OS SGI (all models), DECstation 5000, DEC Alpha, NeXTstation LANGUAGE Graphic_Library: GL, OpenGL, or NextStep VOLUME - REQUIRES - COMMENTS - AC BC00204 NAME NOCUT DOMAIN Restriction maps DOMAIN GCG tools DESCRIPTION Production of restriction enzyme database file DESCRIPTION of non-cutters taken from MAP output for use DESCRIPTION with MAP/SIL. AUTHOR Easton T. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS DCL LANGUAGE C VOLUME - REQUIRES GCG AC BC00207 NAME ACCESS DOMAIN Searching databases DOMAIN GCG tools DESCRIPTION Locate entry in Protein or Nucleic sequence DESCRIPTION Databases by means of the Accession Number or DESCRIPTION the Sequence Identification. Answers the DESCRIPTION question: Where is and how can I retrieve the DESCRIPTION sequence M10112 ? AUTHOR Prilusky J. RT - ADDRESS Weizmann Institute of science ADDRESS P.O.B. 26, Rehovot 76100, Israel CONTACT lsprilus@weizmann.weizmann.ac.il SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk OS Vax/Vms Unix LANGUAGE Pascal VOLUME - REQUIRES requires GCG 7.0 AC BC00225 NAME EASYMENU DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION Provides a menu driven access to the programs DESCRIPTION contained into the Genetics Computer Group's DESCRIPTION package. AUTHOR Prilusky J. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS DCL (VAX Command Language)requirements GCG 7.0 LANGUAGE C VOLUME - AC BC00226 NAME EGCG DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION EGCG is a package of 65 programs which extend the programs DESCRIPTION in the current GCG package and add many entirely new functions. DESCRIPTION Many of the programs were previously available as "GCGEMBL" DESCRIPTION in the UNSUPPORTED.BCK saveset on the GCG distribution for VMS. DESCRIPTION As the programs are no longer entirely written at EMBL, the name DESCRIPTION of the package have changed . The "E" stands for "Extended" GCG. DESCRIPTION 26 new programs in this VMS release (* indicates programs DESCRIPTION included in the Unix release distributed by GCG on CD-ROM with DESCRIPTION GCG version 7.2) DESCRIPTION AllTrans : Translates a set of aligned DNA sequences into aligned DESCRIPTION protein sequences. DESCRIPTION *BasePairPlot : Plots the % occurrence and obs/expected frequency DESCRIPTION of any dinucleotide pair i a sequence DESCRIPTION BFastA : A version of FastA using the BLOSUM62 matrix. DESCRIPTION BTFastA : A version of TFastA using the BLOSUM62 matrix. DESCRIPTION *DbStats : Reports database statistics. DESCRIPTION *GelFigure : Produces a graphical report of a contig in a DESCRIPTION Fragment Assembly project, including restriction map, open DESCRIPTION reading frames and fragment alignment. DESCRIPTION *KabatToGcg : Converts the KABAT database to GCG format. DESCRIPTION MapSelect : Selects restriction enzymes by name or by ability to DESCRIPTION cut a specified sequence, and creates a new ENZYME.DAT file for DESCRIPTION use by other programs. DESCRIPTION *Melt : Calculates the melting temperature and %GC of a sequence. DESCRIPTION *MeltPlot : Plots the melting curve for a nucleic acid sequence. DESCRIPTION NewFeatures : An interactive editor for entering and modifying DESCRIPTION the feature table, and for minor editing of the sequence itself. DESCRIPTION Also able to understand most feature table syntax, including DESCRIPTION joins across entries and additional qualifiers. DESCRIPTION NoReturn : Removes trailing carriage returns and line feeds. DESCRIPTION *Palindrome : Searches for perfect inverted repeats. DESCRIPTION PepAllWindow : Plots hydrophobicity for one or more multiple DESCRIPTION sequence alignments. DESCRIPTION PepCoil : Identifies potential coiled-coil regions in proteins. DESCRIPTION *PlotAlign : Plots conserved properties at each position in a DESCRIPTION multiple sequence alignment. DESCRIPTION *SeqDbToGcg : Converts the SEQDB database to GCG format. DESCRIPTION ToEmbl : Extracts an EMBL entry in EMBL format. DESCRIPTION ToGenBank : Extracts a GenBank entry in GenBank format. DESCRIPTION ToPirAll : Converts a set of sequences of subsequences into a DESCRIPTION single file in PIR format. DESCRIPTION *ToText : Converts a sequence to plain text. DESCRIPTION TProfileGap : ProfileGap with optional 6-frame translation of a DESCRIPTION DNA sequence. DESCRIPTION TProfileSearch : ProfileSearch with ability to search any size of DESCRIPTION database, and optional 6-frame translation of DNA databases. DESCRIPTION TProfileSegments : [1,2] Processes the output file from DESCRIPTION TProfileSearch. DESCRIPTION TSegments : Processes TWordSearch output. DESCRIPTION TWordSearch : WordSearch with a 6-frame translation of the DESCRIPTION database. DESCRIPTION 19 GCG programs with command line control DESCRIPTION Command line control has been added to all the GCG programs that DESCRIPTION did not provide full support. This work was done by summer DESCRIPTION student Jaakko Hattula from Tampere University of Technology in DESCRIPTION Finland. The programs (see the GCG manual for details) are: DESCRIPTION EAssemble, ECodonFrequency, ECompTable, EConsensus, ECorrespond, DESCRIPTION ECrypt, EDiverge, EExtractPeptide, EFingerPrint, EFromStaden, DESCRIPTION EGetSeq, EPublish, ERepeat, EReverse, EStatPlot, ETerminator, DESCRIPTION EToStaden, ETranslate, EWindow DESCRIPTION 20 programs from the original GCGEMBL package, many now enhanced: DESCRIPTION Antigenic : Reports potential antigenic regions. DESCRIPTION CheckLen : Calculates checksums for entries in a database. DESCRIPTION CheckLenComp : Compares CheckLen output for two databases, and DESCRIPTION reports a list of unique entries. DESCRIPTION CpGPlot : Plots the frequency of occurrence of CG dinucleotides DESCRIPTION and percentage of C and G in a sequence. DESCRIPTION FastACheck : Selects significant alignments from (T)Fasta output DESCRIPTION files. DESCRIPTION GbOnly : Creates a list of GenBank entries that have accession DESCRIPTION numbers not found in the latest EMBL release. DESCRIPTION GelAnalyze : Reads the output of GelStatus, and produces project DESCRIPTION statistics for shotgun sequencing. DESCRIPTION GelPicture : Displays a diagram and printout of a contig from a DESCRIPTION Fragment Assembly project, with ambiguities highlighted. DESCRIPTION GelStatus : Reports progress of a Fragment Assembly project. DESCRIPTION HelixTurnHelix : Predicts helix-turn-helix DNA binding domains. DESCRIPTION NewQuickIndex : A much faster version of QuickIndex that produces DESCRIPTION the index files for NewQuickSearch. DESCRIPTION NewQuickSearch : A much faster version of QuickSearch that can DESCRIPTION run on almost all systems without a major virtual memory DESCRIPTION overhead. DESCRIPTION PepNet : Displays part of a protein as a helical net. DESCRIPTION PepStats : Gives a short statistical summary on the composition DESCRIPTION of a protein sequence, or a 3-franme translation. DESCRIPTION PepWheel : Displays part of a protein as a helical wheel. DESCRIPTION PepWindow : Plots hydrophobicity of a protein sequence. DESCRIPTION PirOnly : Selects entries from PIR that are not in the latest DESCRIPTION Swiss-Prot release. DESCRIPTION PrettyPlot : Displays multiple sequence alignments with boxes DESCRIPTION around conserved regions. DESCRIPTION QuickMatch : Displays the overlaps found by NewQuickSearch DESCRIPTION (or by QuickSearch), with selection for good quality matches. DESCRIPTION SigCleave : Predicts signal peptide cleavage sites. AUTHOR Version 7.2 of the EGCG Programs was prepared by AUTHOR Peter Rice (EMBL, Heidelberg, Germany), Rodrigo Lopez AUTHOR (Biotechnology Centre of Oslo, Norway), Jaakko Hattula AUTHOR (Tampere University of Technology, Finland),Reinhard Doelz AUTHOR (Basel, Switzerland) and Jack Leunissen (CAOS/CAMM Centre, AUTHOR Netherlands). RA Gibson T.J., Rice P.M., Thompson J.D., Heringa J.; RT "KH domains within the FMR1 sequence suggest that RT fragile X syndrome stems from a defect in RNA metabolism."; RL Trends Biochem. Sci. 18:331-333(1993). RX Medline; 94054651. RA Musacchio A., Gibson T., Rice P., Thompson J., Saraste M.; RT "The PH domain: a common piece in the structural RT patchwork of signalling proteins."; RL Trends Biochem. Sci. 18:343-348(1993). RX Medline; 94054654. ADDRESS - CONTACT Peter Rice Peter.Rice@sanger.ac.uk CONTACT Rodrigo Lopez rodrigol@biotek.uio.no SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax/egcg SITE by E-mail from the EMBL Network File Server SITE Send E-mail to address NETSERV@ebi.ac.uk with the SITE following message text: SITE HELP SOFTWARE SITE HELP VAX_SOFTWARE SITE GET VAX_SOFTWARE:EGCG.UAA SITE-CONTACT - OS Porting of the EGCG programs from VAX/VMS to ALPHA OpenVMS was OS supported by DEC under a University Porting Agreement. LANGUAGE - VOLUME - AC BC00229 NAME GCGDBASE DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION GCG extensions developed at EMBL for using new DESCRIPTION EMBL distribution format AUTHOR Rice P. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS - LANGUAGE FORTRAN C VOLUME - REQUIRES GCG package v6 AC BC00230 NAME GCGEMBL DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION GCG extensions developed at EMBL AUTHOR Rice P. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS - LANGUAGE FORTRAN C VOLUME - REQUIRES GCG package v6 AC BC00231 NAME GCGMENU DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION Extendable menu interface to GCG package AUTHOR Gartmann, C. RA Gartmann C.J., Grob U.; RT "A menu-shell for the GCG programs."; RT Comput. Appl. Biosci. 7:457-460(1991). RX Medline; 92083354. RX SeqAnalRef; GARC9101. ADDRESS Max-Planck-Institut fur Immunbiologie, Freiburg, FRG. CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk OS - LANGUAGE FORTRAN C VOLUME - REQUIRES GCG package v7.0 AC BC00232 NAME GCGQUICK DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION GCG extensions developed at EMBL for speeding DESCRIPTION up QuickSearch AUTHOR Rice P. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS - LANGUAGE FORTRAN C VOLUME - REQUIRES GCG package v6 AC BC00233 NAME GCGSHELLS1 DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION DCL shells for many GCG programs AUTHOR Clark S. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS DCL, requirements : VAX Fortran LANGUAGE FORTRAN C VOLUME - AC BC00234 NAME GCGSHELLS2 DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION DCL shells to facilitate GenBank on-line DESCRIPTION service access AUTHOR Clark S. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS VAX/VMS LANGUAGE DCL, VAX FORTRAN C VOLUME - AC BC00235 NAME GCG Wisconsin Package DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION Editing , Fragment Assembly , Mapping DESCRIPTION Comparison , Sequence Database Searching , DESCRIPTION Multiple Sequence Analysis , DESCRIPTION Pattern Recognition , RNA Secondary Structure DESCRIPTION Protein Analysis , Translation , Manipulation DESCRIPTION Display , Sequence Exchange File Utilities AUTHOR - RT - ADDRESS Genetics Computer Group, USA ADDRESS 575 Science Drive, Madison, Wisconsin 53711 U.S.A. DDRESS Tel: 1-608-231-5200. Fax: 1-608-231-5202. CONTACT Dina A. Beers (Customer Relations) : Beers@gcg.com CONTACT help@gcg.com OS VAX or AXP with OpenVMS 6.1, AXP (RISC) with OSF/1 2.0, OS IBM (RISC) with AIX 3.2.5, SGI (RISC) with Irix 5.2, OS Sun (Sparc) with Solaris 2.3 LANGUAGE Fortran, C VOLUME - AC BC00245 NAME MENUGCG DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION Menu interface to GCG package AUTHOR Marc Colet RT - ADDRESS BEN ADDRESS Rue des Chevaux 67, 1640 Rhode-Saint-Genese, BELGIUM CONTACT mcolet@dbm.ulb.ac.be SITE ftp anonymous ftp.be.embnet.org SITE Directory /pub/menugcg SITE as archive (tar) files compressed (.Z). SITE-CONTACT gbottu@dbm.ulb.ac.be OS Unix LANGUAGE csh script VOLUME - REQUIRES GCG v8 or 9 AC BC00257 NAME SQUIRREL DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION SQUIRREL is a set of programs to analyze signal regions in DNA DESCRIPTION sequences. The method is based on sequence consensus matrices. DESCRIPTION A signal is composed of several signal blocks separated from DESCRIPTION each other by variable distances. DESCRIPTION Programs are provided to align and create block matrices and DESCRIPTION to search for signals in larger sequences. DESCRIPTION The programs provide a full-screen user-interface with online DESCRIPTION help. DESCRIPTION GCG, although not necessary, is highly recommended. AUTHOR Ch. Gartmann & U. Grob RA Gartmann C.J., Grob U.; RT "SQUIRREL: Sequence QUery, Information Retrieval and REporting RT Library. A program package for analyzing signals in nucleic RT acid sequences for the VAX."; RL Nucleic Acids Res. 19(21):6033-6040(1991). RX Medline; 92051397. RX SeqAnalRef; GARC9102. ADDRESS Christoph Gartmann, Max-Planck-Institut fuer Immunbiologie ADDRESS Freiburg, FRG CONTACT gartmann@immunbio.mpg.de SITE - SITE-CONTACT - OS VAX - VMS LANGUAGE Pascal VOLUME - AC BC00274 NAME PDBTOGCG DOMAIN Sequence format conversion tools DOMAIN GCG tools DESCRIPTION Extracts protein squences from PDB files AUTHOR Mezei M. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk OS VAX/VMS LANGUAGE FORTRAN VOLUME - AC BC00276 NAME PROSITEC DOMAIN Sequence format conversion tools DOMAIN GCG tools DESCRIPTION Conversion of Prosite database to GCG Find DESCRIPTION format AUTHOR Hofmann K. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS VAX/VMS LANGUAGE Pascal VOLUME - AC BC00280 NAME TDF2GCG DOMAIN Sequence format conversion tools DOMAIN GCG tools DESCRIPTION Program to convert the SITES table of the TFD DESCRIPTION database to GCG format. AUTHOR Mathog D. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk OS Vax/VMS LANGUAGE FORTRAN C VOLUME - REQUIRES GCG package AC BC00285 NAME AMPHI DOMAIN Structure prediction DOMAIN GCG tools DESCRIPTION Prediction of membran protein structure AUTHOR Jaehnig F. RX Medline; 90223529. RX SeqAnalRef; JAHF9001. RA Jahnig F.; RT "Structure predictions of membrane proteins are not that bad."; RL Trends Biochem. Sci. 15:93-95(1990). ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison dbd@theory.bchs.uh.edu OS Vax/VMS LANGUAGE FORTRAN VOLUME - REQUIRES GCG v6 for plotting AC BC00342 NAME NCBISHELLS DOMAIN e-mail Server RETRIEVAL and ANALYSIS DOMAIN GCG tools DESCRIPTION DCL shells for using NCBI BLAST, record search, DESCRIPTION and sequence retrieval services. AUTHOR Macrides F. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/vax SITE-CONTACT Don Gilbert: gilbertd@cricket.bio.indiana.edu SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS Vax/VMS LANGUAGE FORTRAN C DCL VOLUME - REQUIRES GCG(v7.0 or higher) AC BC00572 NAME WWW2GCG DOMAIN GCG tools DOMAIN Sequence analysis DESCRIPTION WWW interface to GCG package AUTHOR Marc Colet RA Colet M., Herzog R.; RT "WWW2GCG, a web interface to the GCG biological sequences RT analysis software"; RL Comput. & Graphics 20:445-450(1996). ADDRESS BEN ADDRESS Rue des Chevaux 67, 1640 Rhode-Saint-Genese, BELGIUM CONTACT mcolet@dbm.ulb.ac.be SITE ftp anonymous ftp.be.embnet.org SITE Directory /pub/www2gcg SITE-CONTACT gbottu@dbm.ulb.ac.be OS Solaris, DEC UNIX,SGI IRIX LANGUAGE C,Perl, JavaScript, Java VOLUME - REQUIRES GCG v9, WWW server, Perl v5 COMMENTS contains sequence editor Java applet : ROASTED COMMENTS displays graphics using licenced GIF driver or COMMENTS (included in distribution) Fig2Java of Hayashi & Miyajima AC BC00590 NAME FASTA SCAN DOMAIN Sequence format conversion tools DOMAIN Sequence tools DOMAIN GCG tools DOMAIN Alignment editing and display DOMAIN Alignment browser DESCRIPTION FASTA SCAN allow you to select and save sequences of real DESCRIPTION interest from a FASTA output. DESCRIPTION This version was successfully tested with: DESCRIPTION - FASTA of GCG package (v.8.1 and 10) DESCRIPTION - FASTA of "Pearson package" version 3.1t07 May, 1998 DESCRIPTION The maximum number of sequences is 1000. AUTHOR Olivier Friard RT - ADDRESS Dipartimento di Genetica, Biologia e Biochimica ADDRESS via Santena, 5bis ADDRESS I-10126 TURIN ITALY CONTACT friard@molinette.unito.it SITE WWW Server at URL http://pcgen018.molinette.unito.it/programs.html OS win95, win98, NT 4.0 LANGUAGE - VOLUME - REQUIRES -