Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00263 NAME RSVP DOMAIN Sequence display DESCRIPTION RSVP: Rapid Sequence Visualization in PostScript DESCRIPTION RSVP is a tool for visualization of short DNA sequences, DESCRIPTION implemented in PostScript AUTHOR David Searls RA Searls D.B.; RT "Doing sequence analysis with your printer."; RL Comput. Appl. Biosci. 9:421-426(1993). RX Medline; 94005761. RX SeqAnalRef; SEAD9301. ADDRESS Department of Genetics, ADDRESS University of Pennsylvania School of Medicine, ADDRESS Philadelphia 19104-6145, USA. CONTACT rsvp@cbil.humgen.upenn.edu SITE ftp anonymous cbil.humgen.upenn.edu SITE Directory /pub/rsvp SITE-CONTACT - OS - LANGUAGE Postscript sh VOLUME - AC BC00427 NAME DataMinder DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Oligomer design and synthesis DOMAIN Database and analysis DESCRIPTION DataMinder is a standalone data management program designed DESCRIPTION for molecular biologists. One can readily store and retrieve DESCRIPTION data about oligonucleotides, nucleic acid or protein DESCRIPTION sequences, recombinant DNA clones, cells, reagents and DESCRIPTION protocols .A number of utilities for data analysis are provided, DESCRIPTION including those for calculating the Tms of oligonucleotides and DESCRIPTION for the evaluation of oligonucleotides for use as DESCRIPTION hybridization probes or primers for DNA synthesis. A DESCRIPTION variety of sequence editing features including voice veri- DESCRIPTION fication and the ability to import and export sequence data DESCRIPTION in a variety of different formats are also provided.Context- DESCRIPTION sensitive help is provided. DataMinder is simple to use and to DESCRIPTION customize and allows for sharing of database information DESCRIPTION across a computer network. AUTHOR Karen Usdin RA Usdin K.; RT "Hypercard-based data management tools for molecular biologists."; RL Comput. Appl. Biosci. 8:107-111(1992). RX Medline; 92274208. RX SeqAnalRef; USDK9201. ADDRESS Building 8, Room 202 ADDRESS 8 Center DR MSC 0830 ADDRESS National Institutes of Health ADDRESS Bethesda, MD 20892-0830 ADDRESS U.S.A. CONTACT ku@helix.nih.gov SITE - SITE-CONTACT - OS MAC LANGUAGE C, hypertalk VOLUME - REQUIRES Mac SE or above, 2MB Ram AC BC00455 NAME Statistical Routines DOMAIN Sequence display DESCRIPTION Routines written for the statistical package Splus in the DESCRIPTION aim of a visual analysis of DNA sequences. Two types of DESCRIPTION charts are produced, random walk plots and gap plots. For DESCRIPTION details, see CABIOS, 11, pp. 503 AUTHOR P.M. Leong, S. Morgenthaler AUTHOR Nestlé Research Centre and EPF Lausanne RA Leong P.M., Morgenthaler S.; RT "Random walk and gap plots of DNA sequences."; RL Comput. Appl. Biosci., 11:503-511(1995). ADDRESS EPFL - DMA ADDRESS 1015 Lausanne ADDRESS Switzerland CONTACT morgi@dma.epfl.ch SITE ftp anonymous masg1.epfl.ch SITE Directory /anyone/morgi/dna SITE-CONTACT - OS Unix, Windows LANGUAGE Splus Statistical Package VOLUME - REQUIRES Splus Statistical Package AC BC00461 NAME DNA Stacks DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Pattern Identification DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Genome Mapping Databases DOMAIN Phylogeny DESCRIPTION DNA Stacks (v. 1.1) is a HyperCard 2.x stack package DESCRIPTION for Macintosh computers featuring utilities for editing or DESCRIPTION coloring multiple DNA or protein sequence alignments, DESCRIPTION performing numerous data conversions or analyses related to DESCRIPTION molecular systematics, displaying auto-rescalable gene maps DESCRIPTION of mitochondrial or chloroplast genomes, extracting DNA DESCRIPTION gene sequences or translated protein sequences from about DESCRIPTION 26 animal mitochondrial genomes, and graphically depicting DESCRIPTION codon usage patterns. AUTHOR Eernisse, Douglas J. RA Eernisse, D. J.; RT "DNA Translator and Aligner: HyperCard utilities to aid RT phylogenetic analysis of molecules."; RL Comput. Appl. Biosci. 8:177-184(1992). RX Medline; 92274217. RX SeqAnalRef; EERD9201. ADDRESS D. J. Eernisse ADDRESS Dept. Biol. Sci. MH282 ADDRESS California State University ADDRESS Fullerton, CA 92634, USA CONTACT deernisse@fullerton.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/mac/ SITE-CONTACT archive@bio.indiana.edu SITE gopher Host: gopher://ftp.bio.indiana.edu Port: 70 SITE URL gopher://gopher://ftp.bio.indiana.edu:/70/11/IUBio-Software+Data/molbio/mac SITE WWW Server at URL http://biology.fullerton.edu/people/faculty/doug-eernisse/ OS MacOS LANGUAGE HyperTalk, C VOLUME 2 MB REQUIRES HyperCard 2.0 or greater, Macintosh AC BC00470 NAME Primer Premier 4 DOMAIN Oligomer design and synthesis DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN RNA analysis DOMAIN Restriction maps DESCRIPTION Primer Design Software DESCRIPTION Primer Premier 4 is now available for Power Macintosh and DESCRIPTION Window 3.1, NT as well as Windows 95. Primers can be DESCRIPTION designed for PCR, sequencing or hybridization probes DESCRIPTION automatically or with full manual control. DESCRIPTION From the selected pool of primers mutually compatible DESCRIPTION Nested/Multiplex primers or pairs can be chosen. DESCRIPTION Any primer can be mutated using the editing facility. DESCRIPTION Full degeneracy is supported. Comprehensive analyis of DESCRIPTION secondary structures as well as a table of properties DESCRIPTION including melting temperature calculated using nearest DESCRIPTION neighbor theory and optimal annealing temperature is DESCRIPTION displayed for each primer. DESCRIPTION DESCRIPTION The selected primers can be managed with the database DESCRIPTION storage facility. The program even makes the primer DESCRIPTION synthesis process painless by automatically creating an DESCRIPTION order form addressed to the vendor of your choice. DESCRIPTION DESCRIPTION Restriction enzyme analysis is available with multiple DESCRIPTION output formats: table, annotated sequence or map. Functions DESCRIPTION to edit the sequence and to translate it using standard or DESCRIPTION any mitochondrial/organelle codon table is provided. Graphs DESCRIPTION of melting temperature, internal stability and free energy DESCRIPTION are available on-line as well as in printed format. AUTHOR Premier Biosoft International RT - ADDRESS 3786 Corina Way ADDRESS Palo Alto, CA 94303 CONTACT sales@PremierBiosoft.com SITE WWW Server at URL http://www.PremierBiosoft.com OS Windows 95, 98, NT, 3.1, Power Macintosh LANGUAGE - VOLUME - REQUIRES - COMMENTS Commercial product, fully functional demo available at COMMENTS http://www.PremierBiosoft.com page. AC BC00495 NAME BlueGene DOMAIN Neural Networks DOMAIN Searching databases DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Structure prediction DOMAIN Database and analysis DESCRIPTION BlueGene uses a fast neural network for sequence similarity DESCRIPTION searches in Genbank and SWISS-PROT databases. DESCRIPTION BlueGene also includes graphically tools for sequence DESCRIPTION editing and analysing. DESCRIPTION BlueGene uses given and new sequence features to annotate DESCRIPTION the sequence editor and the map. AUTHOR Magic Works GmbH RT - ADDRESS Magic Works GmbH ADDRESS Potsdamer Str. 18a ADDRESS D-14513 Teltow ADDRESS GERMANY CONTACT info@magic-works.com SITE WWW Server at URL http://www.bluegene.com/ SITE-CONTACT - OS Win 3.1x or higher LANGUAGE - VOLUME 3.1MB REQUIRES 16MB RAM COMMENTS A free BlueGene demo version is ready for downloading on COMMENTS http://www.bluegene.com/. AC BC00497 NAME Sequin DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Sequence data submissions DESCRIPTION Sequin is a stand-alone software tool developed by the NCBI DESCRIPTION for submitting entries to the GenBank, EMBL, or DDBJ DESCRIPTION sequence databases. It is capable of handling simple DESCRIPTION submissions which contain a single short mRNA sequence, and DESCRIPTION complex submissions containing long sequences, multiple DESCRIPTION annotations, segmented sets of DNA, or phylogenetic and DESCRIPTION population studies. AUTHOR Jonathan Kans, Colombe Chappey RT - ADDRESS NIH/NLM/NCBI ADDRESS Building 38A, Room 8N805 ADDRESS Bethesda, MD 20894 ADDRESS U.S.A. CONTACT info@ncbi.nlm.nih.gov SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /sequin SITE-CONTACT info@ncbi.nlm.nih.gov SITE WWW Server at URL http://www.ncbi.nlm.nih.gov/Sequin OS Mac (68K and PPC), Windows (16 and 32 bit), Unix (Sun, Solaris, SGI, Linux, DEC) LANGUAGE English VOLUME - REQUIRES - COMMENTS Information about this package is available from COMMENTS http://www.ncbi.nlm.nih.gov/Sequin AC BC00533 NAME DNAmend DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Genetic tools DOMAIN Restriction maps DESCRIPTION DNAmend is cloning software. That means, it may serve DESCRIPTION lab-workers in molecular biology and genetic engineering to DESCRIPTION monitor the DNA-cloning process. The PC routine provides DESCRIPTION on-line control on the steps of a cloning protocol - DESCRIPTION including the selection of the vectors and fragments, their DESCRIPTION processing by restrictase digestion, subsequent ligation, DESCRIPTION and the analysis of the cloned DNA. DESCRIPTION The software is designed to accept files containing DNA DESCRIPTION sequence information in any file format based on PC-text. DESCRIPTION A set of pull-down menu commands enables the user to change DESCRIPTION the mode of viewing the DNA-sequences, print them out, and DESCRIPTION above all manipulate them. One can search DNA sequences for DESCRIPTION restriction sites, open reading frames and certain sequence DESCRIPTION patterns, translate the sequences and simulate Restriction, DESCRIPTION Ligation or End modification on-line. DESCRIPTION One may export maps of the DNA-sequences via clipboard into DESCRIPTION other Windows applications to prepare them for publishing. DESCRIPTION The program contains a detailed on-line help. AUTHOR Piet Jonas & Bjoern Maul - ADDRESS Dr. Bjoern Maul ADDRESS B.-Lichtenberg-Str. 10 ADDRESS 10407 Berlin ADDRESS Germany CONTACT maul@fmp-berlin.de SITE WWW Server at URL http://pc13mi.biologie.uni-greifswald.de/sequenz.html OS Microsoft Windows LANGUAGE Turbo Pascal VOLUME 500 KB disc space REQUIRES IBM-PC, 4 MB RAM, Windows 3.x/95/NT COMMENTS Download a free Demo-Version at COMMENTS http://pc13mi.biologie.uni-greifswald.de/sequenz.html AC BC00535 NAME VECTOR NTI DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Genome Mapping Databases DOMAIN Restriction maps DESCRIPTION Software package for molecular biology. DESCRIPTION Vector NTI is a software package to aid DESCRIPTION molecular biologists, genetic engineers, students, and DESCRIPTION others in the study, manipulation, and creation of DESCRIPTION biological molecules. It's extremely helpful in supporting DESCRIPTION your everyday lab work, making it mistake free and saving DESCRIPTION enormous amounts of your time. Using vector NTI you can: DESCRIPTION automatically create an optimum cloning strategy for DESCRIPTION construction and design of new genetic molecules, perform DESCRIPTION advanced PCR, oligo and primer analysis, organize your DESCRIPTION biological data (molecules, oligos, ect.) using a DESCRIPTION professional database, create excellent publication quality DESCRIPTION graphical molecule maps, transfer changes made to molecules DESCRIPTION in child/parent trees, run dynamic electrophoresis, predict DESCRIPTION runtime, connect to Oracle backend database and much much DESCRIPTION more. Free demo at informaxinc.com AUTHOR InforMax Inc. RT - ADDRESS 6110 Executive Blvd suite 400 ADDRESS North Bethesda, Maryland 20852, USA ADDRESS +1 301 216-0586 ADDRESS +1 301 216-0087 fax CONTACT - SITE WWW Server at URL http://informaxinc.com OS Mac68k/PPC, Win 95/NT/3.1 LANGUAGE - VOLUME - REQUIRES - AC BC00541 NAME Plasmid Premier DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Restriction maps DESCRIPTION PLASMID PREMIER is a fully featured vector analysis and DESCRIPTION publication quality graphics tool. It provides vector DESCRIPTION analysis tools including restriction enzymes, motifs, DESCRIPTION open reading frames, and features. It allows complete DESCRIPTION restriction enzyme analysis including user defined enzymes, DESCRIPTION enzyme filtering by overhang and cutting frequency, and a DESCRIPTION databases of over 300 enzymes. Motif analysis automatically DESCRIPTION locates motifs such as TACCC-binding and T-antigen sequences DESCRIPTION and supports user defined motifs. ORF analysis locates all DESCRIPTION open reading frames in both the sense and anti-sense DESCRIPTION direction. Start and stop codons are editable allowing DESCRIPTION support of mitochondrial codon tables. Features from GenBank DESCRIPTION files are automatically read and shown on the plasmid. DESCRIPTION DESCRIPTION In addition to automatic analysis, enzymes, motifs, and DESCRIPTION features can be added manually. The user can set position, DESCRIPTION font, and color. Default styles can be set and modified. DESCRIPTION Styles can be copied and pasted between objects. Plasmids DESCRIPTION can be output in Windows bitmap or Mac PICT formats, or cut DESCRIPTION and pasted through the clipboard. AUTHOR PREMIER Biosoft International RT - ADDRESS 3786 Corina Way ADDRESS Palo Alto, CA 94303-9504 ADDRESS U.S.A. CONTACT sales@PremierBiosoft.com SITE WWW Server at URL http://www.PremierBiosoft.com OS Windows 95, Windows 98, Windows NT LANGUAGE C++ VOLUME 1.4 MB REQUIRES - COMMENTS Commercial product, fully functional demo available at COMMENTS http://www.PremierBiosoft.com page. AC BC00552 NAME ESSA DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN RNA analysis DOMAIN WWW server DESCRIPTION With ESSA, we propose an approach of RNA secondary DESCRIPTION structure analysis based on extensive viewing within a DESCRIPTION friendly graphical interface. This computer program is DESCRIPTION organized around the display of folding models produced by DESCRIPTION two complementary methods suitable to draw long RNA DESCRIPTION molecules. Any feature of interest can be managed directly DESCRIPTION on the display and highlighted by a rich combination of DESCRIPTION colours and symbols with emphasis given to structural probe DESCRIPTION accessibilities. ESSA also includes a word searching DESCRIPTION procedure allowing easy visual identification of structural DESCRIPTION features even complex and degenerated. Analysis functions DESCRIPTION make it possible to calculate the thermodynamic stability DESCRIPTION of any part of a folding using several models and compare DESCRIPTION homologous aligned RNA both in primary and secondary DESCRIPTION structure. The predictive capacities of ESSA which brings DESCRIPTION together the experimental, thermodynamic and comparative DESCRIPTION methods, are increased by coupling it with a program DESCRIPTION dedicated to RNA folding prediction based on constraints DESCRIPTION management AUTHOR Chetouani F., Monestie P., Thebault P., Gaspin C., Michot B. RA Chetouani F., Monestie P., Thebault P., Gaspin C., Michot B.; RT "ESSA: An integrated and interactive computer tool for RT analysing RNA secondary structure."; RL Nucleic Acids Res 25(17):3514-3522(1997). ADDRESS Gaspin : Station de Biometrie et d'Intelligence Artificielle, ADDRESS I.N.R.A., Chemin de Borde-Rouge, Auzeville BP 27, 31326 ADDRESS Castanet-Tolosan Cedex, FRANCE ADDRESS tel : (33) 05 61 28 52 82; fax : (33) 05 61 28 53 35; ADDRESS e-mail : gaspin@toulouse.inra.fr ADDRESS Michot, Chetouani ADDRESS Laboratoire de Biologie Moleculaire Eucaryote du C.N.R.S., ADDRESS Universite Paul Sabatier, 118 route de Narbonne, ADDRESS 31062 Toulouse Cedex, FRANCE ADDRESS tel : (33) 05 61 33 58 65; fax : (33) 05 61 33 58 86; ADDRESS e-mail : bmichot@ibcg.biotoul.fr farid@ibcg.biotoul.fr CONTACT essa@toulouse.inra.fr SITE WWW Server at URL http://www-bia.inra.fr/T/essa/Doc/essa_home.html OS UNIX : SUN, SGI, HP LANGUAGE C VOLUME 200 Kb REQUIRES - AC BC00554 NAME Plasmid Processor DOMAIN Sequence display DESCRIPTION Plasmid Processor is a simple tool for plasmid presentation DESCRIPTION for scientific and educational purposes. It features both DESCRIPTION circular and linear DNA, user defined restriction sites, DESCRIPTION genes and multiple cloning site. In addition you can DESCRIPTION manipulate plasmid by inserting and deleting fragments. DESCRIPTION Created drawings can be copied to clipboard or saved to disk DESCRIPTION for later use. Printing from within program is also DESCRIPTION supported. DESCRIPTION Plasmid Processor is freeware, so you can use and DESCRIPTION distribute it freely. DESCRIPTION Plasmid Processor program was created during a programming DESCRIPTION project course held in Department of Computer Sciences and DESCRIPTION Applied Mathematics, University of Kuopio, Finland AUTHOR T. Kivirauma, P. Oikari and J. Saarela. RT - ADDRESS - CONTACT plasmid@uku.fi. SITE WWW Server at URL http://www.uku.fi/~kiviraum/plasmid/plasmid.html OS Win95, WinNT, Windows 3.1 LANGUAGE - VOLUME - REQUIRES - COMMENTS Good little program for drawing plasmid maps - not as COMMENTS powerful as DNA Strider but free! AC BC00587 NAME BioEdit DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN RNA analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Searching databases DOMAIN General tools DESCRIPTION BioEdit is a user-friendly, graphically-oriented sequence DESCRIPTION alignment editor for Windows 95/98/NT. Features include DESCRIPTION several modes of hand alignment, auto-linking to ClustalW, DESCRIPTION user-defined color view (editable by mouse point- and DESCRIPTION click), separate amino acid and nucleotide color tables, DESCRIPTION Shaded views with many options, RNA comparative analysis DESCRIPTION tools (including mutual information with interactive 2-D DESCRIPTION matrix plots and area plots), restriction mapping, browsing DESCRIPTION restriction enzymes by company, easy plasmid drawing and DESCRIPTION annotation, protein hydropathy plots, can handle very large DESCRIPTION alignments (up to 20000 sequences of undefined length), DESCRIPTION several translation modes, nucleotide/translation toggling DESCRIPTION for alignment in both protein and DNA views, 6-frame DESCRIPTION translations, basic sequence manipulations (complement, DESCRIPTION reverse, uppercase, lowercase), internal web browser (HTML DESCRIPTION 2.0-compliant), auto-link to external browser with internet DESCRIPTION bookmarks, on-line help system, configure external apps via DESCRIPTION a graphical interface to automatically run through a DESCRIPTION BioEdit interface, split-window views for editing of two DESCRIPTION different places in an alignment at the same time, local DESCRIPTION NCBI BLAST accessories, single sequence editing and DESCRIPTION manipulation, retains GenBank data (eg, FEATURES, DESCRIPTION REFERENCE, SOURCE, PID or NID, etc), binary file format for DESCRIPTION fast save/open of very large files (alignments up to 100 Mb DESCRIPTION and more are no problem), correct spacing of all available DESCRIPTION fonts in edit window and in shaded view, creation of DESCRIPTION high-quality alignment figures via shading with many DESCRIPTION options (including full-color, id/sim shading, enhanced DESCRIPTION metafile copy and paste directly into graphics programs), DESCRIPTION easy formatted text print preview. AUTHOR Tom Hall RT - ADDRESS Department of Microbiology, ADDRESS North Carolina State University ADDRESS Raleigh, NC 27695 CONTACT tahall2@unity.ncsu.edu SITE WWW Server at URL http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html OS Windows LANGUAGE - VOLUME BioEdit.zip file = 7.6 Mb REQUIRES Windows 95, 98 or NT, Pentium 60+, 16 Mb RAM+, REQUIRES 20 Mb hard drive space AC BC00588 NAME DAMBE (Data analysis in molecular biology and evolution) DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Genetic tools DOMAIN Molecular Evolution DOMAIN Phylogeny DOMAIN Database and analysis DOMAIN Searching databases DOMAIN General tools DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION DAMBE (Data Analysis in Molecular Biology DESCRIPTION and Evolution) is an integrated software package for DESCRIPTION converting, manipulating, statistically and graphically DESCRIPTION describing and analyzing molecular sequence data, with a DESCRIPTION user-friendly Windows 95 interface. AUTHOR Xuhua Xia RT - ADDRESS Department of Ecology & Biodiversity, ADDRESS University of Hong Kong, Hong Kong CONTACT xxia@hkusua.hku.hk SITE WWW Server at URL http://web.hku.hk/~xxia/software/software.htm OS Windows 95 LANGUAGE - VOLUME 10 MB REQUIRES Windows 95 AC BC00593 NAME pDRAW32 DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Restriction maps DESCRIPTION Freeware software for various forms of DNA analysis, DESCRIPTION virtual DNA cloning, graphics generation, DESCRIPTION PCR temperature calculation, XY-dotblots and more. AUTHOR Kjeld Olesen, Acaclone Software RT - ADDRESS - CONTACT Kjeld Olesen, acaclone@hotmail.com SITE WWW Server at URL http://www2.crosswinds.net/~acaclone OS Windows 95 or newer LANGUAGE - VOLUME 3 MB REQUIRES - AC BC00594 NAME Protein Adviser for Windows DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Molecular modelling and graphics DOMAIN General tools DOMAIN Chemistry DOMAIN Image analysis DOMAIN Comparative analysis DOMAIN Protein 3D visualisation, editing and analysis (QSAR) DESCRIPTION FQS Protein Adviser displays and analyses 3D structures of DESCRIPTION biological molecules such as proteins or nucleic acids. DESCRIPTION Protein Adviser is a powerful tool for visual and numerical DESCRIPTION investigation of protein molecules and their 3D structures. DESCRIPTION The new implementation for Windows 95/98 and NT uses the DESCRIPTION innovative Microsoft technology for rendering molecular DESCRIPTION graphics known as Direct3D. Using Direct 3D technology FQS DESCRIPTION created the fastest biomolecular viewer available on PC DESCRIPTION platform. DESCRIPTION Versatile features to support protein analysis: DESCRIPTION - sequence based 3D analysis DESCRIPTION - Three level selections: atoms, residues, molecules DESCRIPTION - Display/Hide hydrogen's DESCRIPTION - Display/Hide side chain DESCRIPTION - Hydrogen generation DESCRIPTION - Measure atom-atom distances DESCRIPTION - Compare 3D structures DESCRIPTION - Compare aminoacid sequences DESCRIPTION - Analyze Ramachandran plots DESCRIPTION - Mutate and change side chain conformations DESCRIPTION - Build proteins, change torsional angles DESCRIPTION - Copy and paste molecules between the windows DESCRIPTION - Rotate and move selected molecules DESCRIPTION Windows specific features DESCRIPTION Protein Adviser can open as many documents DESCRIPTION as you wish and analyse them within one program session, DESCRIPTION Protein Adviser implements full ActiveX/OLE2 functionality. DESCRIPTION Its objects (molecules) may be placed on your WEB page and DESCRIPTION visualized by your colleagues everywhere through the DESCRIPTION internet. DESCRIPTION Plotting hydrophobicity and other properties DESCRIPTION Protein Adviser for Windows can plot DESCRIPTION different named properties. The program comes with 3 DESCRIPTION different scales of hydrophobicty, including Kyte&Doolittle DESCRIPTION scale. The program includes also 6 other predefined QSAR DESCRIPTION methods. DESCRIPTION Plotting Ramachandran diagrams DESCRIPTION Ramachandran plots show two-dimensional DESCRIPTION histograms of the values of conformational angles phi and DESCRIPTION psi. These histograms are superimposed on the areas of DESCRIPTION allowed and forbidden conformational angles pair values. DESCRIPTION Aminoacids DESCRIPTION Protein Adviser displays sequences of DESCRIPTION aminoacids as 3-letter codes, 1-letter codes or secondary DESCRIPTION structure symbols DESCRIPTION Protein's 3D structure comparison DESCRIPTION Protein Adviser for Windows allows for DESCRIPTION protein structure comparison command. The program DESCRIPTION superimposes the protein's 3D structures based on C(alpha) DESCRIPTION atoms coordinates and RMSD analysis. AUTHOR FQS Ltd. (Fujitsu Kyushu System Engineering Ltd.) RT - ADDRESS FQS Poland Sp. z o.o. ADDRESS Palac Pugetow ADDRESS ul. Starowislna 13-15 ADDRESS 31-038 Krakow ADDRESS Poland ADDRESS Tel. (+48 12) 4294345 ADDRESS Fax. (+48 12) 4296124 CONTACT info@fqspl.com.pl SITE WWW Server at URL http://www.fqspl.com.pl/protein OS Windows 95/98/NT, Macintosh LANGUAGE English, Japanese VOLUME 10 MB REQUIRES PC Pentium 166, 16MB RAM, Microsoft DirectX COMMENTS Commercial software. COMMENTS Price: COMMENTS 800 USD - commercial license & COMMENTS 400 USD - academic licence AC BC00601 NAME Jalview DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN JAVA DOMAIN Multivariate analysis DOMAIN WWW server SERVER http://circinus.ebi.ac.uk:6543/jalview DESCRIPTION A multiple sequence alignment viewer and editor. Alignments DESCRIPTION can be divided into subfamilies using a tree or by hand. DESCRIPTION Conservation can then be calculated using physico-chemical DESCRIPTION properties within subfamilies or across the whole alignment. DESCRIPTION Principal component analysis can also be used as an DESCRIPTION alternative way of clustering the sequences. An SRS server DESCRIPTION can be used to fetch and display the sequence features and DESCRIPTION any PDB structures listed. There is limited access to DESCRIPTION external programs including clustalw and jnet secondary DESCRIPTION structure prediction. AUTHOR Michele Clamp RT - ADDRESS The Sanger Centre ADDRESS Wellcome Trust Genome Campus ADDRESS Hinxton ADDRESS Cambs. ADDRESS CB10 1SA ADDRESS UK CONTACT michele@sanger.ac.uk SITE WWW Server at URL http://circinus.ebi.ac.uk:6543/jalview OS - LANGUAGE java1.1 VOLUME 300kb REQUIRES Java runtime environment