Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00264 NAME SEQEDT DOMAIN Sequence editor DESCRIPTION Sequence editor, modelled on EDT AUTHOR Gilbert W.A. 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 - 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 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 BC00463 NAME SeqPup DOMAIN Sequence editor DOMAIN Sequence analysis DESCRIPTION SeqPup is a biological sequence editor and analysis program DESCRIPTION usable on the common computer systems including Macintosh, DESCRIPTION MS-Windows and X-Windows. It includes links to network DESCRIPTION services and external analysis programs. DESCRIPTION Features include DESCRIPTION multiple sequence alignment editor DESCRIPTION single sequence editor DESCRIPTION read and write several sequence file formats DESCRIPTION easy hand alignment features including colored bases and sliding DESCRIPTION automatic multiple sequence alignment with ClustalW app DESCRIPTION automatic gel fragment alignment to contigs with CAP app DESCRIPTION phylogenetic analysis of alignments with fastDNAml and LSADT apps DESCRIPTION phylogenetic tree drawing with DrawTree and DrawGram Phylip apps DESCRIPTION consensus, reverse, complement, degap, and distance/similarity operations DESCRIPTION restriction maps DESCRIPTION pretty print of alignments and sequences with boxed and shaded DESCRIPTION regions. DESCRIPTION translate dna to/from protein using various codon tables DESCRIPTION find strings and ORFs DESCRIPTION automatic preference saving DESCRIPTION internet send mail and sequence analysis services by email DESCRIPTION user-definable links to external analysis programs AUTHOR d. gilbert RT - ADDRESS biocomputing--indiana u--bloomington, in usa 47405 CONTACT SeqPup@Bio.Indiana.Edu SITE ftp anonymous iubio.bio.indiana.edu SITE Directory /molbio/seqpup SITE-CONTACT gilbertd@bio.indiana.edu SITE ftp anonymous iubio.bio.indiana.edu SITE Directory /util/dclap/source/ for the source code SITE-CONTACT gilbertd@bio.indiana.edu SITE WWW Server at URL http://iubio.bio.indiana.edu/IUBio-Software+Data/molbio/seqpup/ OS Macintosh, MS Windows, Unix/XWindow LANGUAGE C++ and C VOLUME - REQUIRES - 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 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 BC00577 NAME NetPrimer DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Oligomer design and synthesis DESCRIPTION NetPrimer is a web-based program that analyzes individual or DESCRIPTION pairs of primers. It is available free of charge. DESCRIPTION The program combines the latest primer design algorithms DESCRIPTION with an intuitive interface allowing the user to quickly DESCRIPTION analyze primers. Primers are analyzed for melting temperature DESCRIPTION using the nearest neighbor thermodynamic theory to ensure DESCRIPTION accurate Tm prediction. Primers are analyzed for all DESCRIPTION secondary structures including hairpins, self-dimers, and DESCRIPTION cross-dimers in primer pairs. This analysis ensures DESCRIPTION the availability of the primer for the reaction as well as DESCRIPTION minimizing the formation of primer dimer. DESCRIPTION The program eases quantitation of primers by calculating DESCRIPTION primer molecular weight and optical activity. DESCRIPTION To facilitate the selection of an optimal primer, DESCRIPTION each primer is given a rating based on the stability of its DESCRIPTION secondary structures. Extensive help including algorithms DESCRIPTION and formulae used is available online. A complete analysis DESCRIPTION report can be printed for individual primers or primer pairs. AUTHOR PREMIER Biosoft International RT - ADDRESS 3786 Corina Way, Palo Alto, CA 94303-4504 ADDRESS Tel: 650-856-2703, Fax: 650-843-1250 CONTACT support@PremierBiosoft.com SITE WWW Server at URL www.PremierBiosoft.com/NetPrimer.html OS Windows 95, Windows 98, Windows NT LANGUAGE Java, Javascript VOLUME 1.8 MB REQUIRES - COMMENTS This appears to be the most comprehensive, free primer analysis COMMENTS program available on the Internet. 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 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 -