Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00567 NAME Finder! DOMAIN General tools DESCRIPTION Finder! helps you organise samples that may DESCRIPTION be stored for subsequent retrieval. It keeps a record of DESCRIPTION the rack and position of the sample and will state this DESCRIPTION when the sample number is entered. Up to 100 samples in up DESCRIPTION to 999 racks can be stored in the fully working version, DESCRIPTION which can also utilise a bar-code reader for ease of entry. DESCRIPTION Data backup and restore are included, as are various checks DESCRIPTION on data entry to reduce errors. A limited use version is DESCRIPTION available for download from the web site. AUTHOR J. G. Williams RT - ADDRESS JGW Computing, ADDRESS 11 Bramley Close, ADDRESS Colletts Green, ADDRESS Powick, ADDRESS Worcester. ADDRESS WR2 4SR ADDRESS UK CONTACT jgw.computing@zetnet.co.uk SITE WWW Server at URL http://www.users.zetnet.co.uk/jgw.computing OS DOS, will run under Windows LANGUAGE Clipper VOLUME 500 k REQUIRES PC compatible, minimum 386 AC BC00576 NAME GraphPap DOMAIN General tools DESCRIPTION Tools for laboratory work DESCRIPTION GraphPap is a programme designed to print any kind of DESCRIPTION plotting sheet for manual graphing. A large choice of scales DESCRIPTION is available : cartesian, polar, linear, logarithmic, DESCRIPTION quadratic, gaussian, metric, imperial. All the combinations DESCRIPTION are allowed. The colour and width of lines are adjustable. DESCRIPTION The size, margins and orientation of the printed grids are DESCRIPTION fully customizable. AUTHOR Dr Philippe Marquis RT - ADDRESS Centre hospitalier regional - 57000 METZ - FRANCE CONTACT philimar@easynet.fr SITE WWW Server at URL http://perso.easynet.fr/~philimar/ OS Windows 95/98/NT4 LANGUAGE English VOLUME 174 Kb REQUIRES Pentium - 16 Mb RAM COMMENTS Free and unlimited software AC BC00580 NAME QualCont DOMAIN Quality Control DOMAIN General tools DESCRIPTION QUALCONT is a programme designed for internal quality DESCRIPTION control of manual analytical techniques in clinical DESCRIPTION laboratories. It records the control charts, archives the DESCRIPTION data and calculates the validation ranges. DESCRIPTION Simple access to the main functions by means of icons and DESCRIPTION the on-line help facilities provided means that QUALCONT is DESCRIPTION a programme which can be immediately utilised without DESCRIPTION training by all aboratory personnel who are familiar with DESCRIPTION control charts. DESCRIPTION The number of analytes is unlimited, and each one is DESCRIPTION provided with up to three control levels. The three levels DESCRIPTION are validated simultaneously after display within coloured DESCRIPTION graphics which represent the control ranges of acceptable, DESCRIPTION warning and rejection. These ranges are calculated from DESCRIPTION the previously entered data using Student's t statistic DESCRIPTION with pre-definable probability thresholds. The decision DESCRIPTION limits can be locked to any date interval or remain mobile. DESCRIPTION Four rejection rules are also tested. DESCRIPTION Each QC point may be connected to a comment. Whenever the DESCRIPTION lot number of a control material changes, the statistical DESCRIPTION data of the previous batch are archived and the control DESCRIPTION chart is restarted. Deletion of outliers can be password- DESCRIPTION protected so it may be restricted to senior laboratory DESCRIPTION staff if desired. DESCRIPTION The data file is backed-up from time to time on a DESCRIPTION diskette at a pre-definable interval. A reminder is DESCRIPTION provided when the programme is started if the backup DESCRIPTION interval has been exceeded. At the end of each day, all of DESCRIPTION that day's control results can be displayed and printed. DESCRIPTION Thus daily viewing of the control performance is available DESCRIPTION in each section of the laboratory where the software is in DESCRIPTION use. AUTHOR Dr Philippe Marquis RT - ADDRESS Centre hospitalier - 57000 METZ - FRANCE CONTACT philimar@easynet.fr SITE WWW Server at URL http://perso.easynet.fr/~philimar/ OS Win95/98/NT4 LANGUAGE English VOLUME 263 Kb REQUIRES Pentium - 16 Mb RAM COMMENTS Free and unlimited software COMMENTS French version available at the same URL 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 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 BC00599 NAME Swissknife DOMAIN General tools DESCRIPTION A set of Perl modules which provides DESCRIPTION a fast and reliable object-oriented interface DESCRIPTION to parsing and modifying files in SWISS-PROT format. AUTHOR Henning Hermjakob, Wolfgang Fleischmann, Rolf Apweiler RA Hermjakob, H., Fleischmann, W. and Apweiler A.; RT "Swissknife - "Lazy Parsing" of SWISS-PROT Entries."; RL Bioinformatics, in press (1999). ADDRESS EMBL Outstation - European Bioinformatics Institute ADDRESS Wellcome Trust Genome Campus ADDRESS Hinxton ADDRESS Cambridge CB10 1SD ADDRESS United Kingdom CONTACT hhe@ebi.ac.uk SITE ftp anonymous ftp://ftp.ebi.ac.uk SITE Directory /pub/software/swissprot/Swissknife/ SITE-CONTACT support@ebi.ac.uk OS - LANGUAGE Perl VOLUME - REQUIRES -