Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00201 NAME COMAP DOMAIN Restriction maps DESCRIPTION programm for helping with the construction of DESCRIPTION restriction maps of small DNA fragment from digestion DESCRIPTION data. The program works under a graphical user DESCRIPTION interface, similar to the one used with the protein DESCRIPTION analysis program PROFILEGRAPH. AUTHOR Hofmann K AUTHOR khofmann@cipvax.biolan.uni-koeln.de RT - ADDRESS Universitaet Koeln , Germany CONTACT - SITE ftp anonymous src.doc.ic.ac.uk SITE Directory /usenet/comp.archives/auto/bionet.software SITE-CONTACT - OS - LANGUAGE - VOLUME - AC BC00202 NAME DOUBLE-DIGESTER DOMAIN Restriction maps DESCRIPTION Double Digester ("DD") is a program designed DESCRIPTION to help researchers in molecular biology DESCRIPTION assemble restriction maps of DNA using data DESCRIPTION from double digest experiments. DESCRIPTION This is an interactive, graphics-based program AUTHOR Wright L. RT - ADDRESS Medical Informatics Center, 3 TMP - Anesthesiology, ADDRESS Yale School of Medicine, New Haven, CT 06510-3333, USA CONTACT wright-lawrence@yale.edu SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.cs.yale.edu SITE Directory /pub SITE-CONTACT - SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/restrict-enz SITE-CONTACT D Gilbert : gilbertd@cricket.bio.indiana.edu OS Sun Sparcstations (up to SunOS 4.1.3), OS HP workstations OS Macintosh computers System 6 or 7.0/7.1 LANGUAGE C Lisp using CLIM VOLUME - AC BC00203 NAME GMAP DOMAIN Restriction maps DESCRIPTION Search translationally silent restriction DESCRIPTION sites that have allowable mismatches DESCRIPTION (for gene synthesis) AUTHOR Raghava G.P.S. RL Biotechniques, 16, 1116-1123. ADDRESS - CONTACT raghava@koel.imtech.ernet.in or raghava@bioch.ox.ac.u 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 C VOLUME - 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 BC00205 NAME RENZYME DOMAIN Restriction maps DESCRIPTION Restriction mapping program based on a fast DESCRIPTION finite state machine pattern matcher. In DESCRIPTION general, the rate at which it finds DESCRIPTION restriction sites is only limited by how fast DESCRIPTION it can read the sequence file in and print out DESCRIPTION the results. AUTHOR Roy Smith RA Smith R.; RT "A finite state machine algorithm for finding restriction sites RT and other pattern matching applications."; RL Comput. Appl. Biosci. 4:459-465(1988). RX Medline; 89089251. RX SeqAnalRef; SMIR8801. ADDRESS Public Health Research Institute, ADDRESS 455 First Avenue, Room 1074, New York, NY 10016, USA. CONTACT Roy Smith roy@alanine.phri.nyu.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/restrict-enz SITE-CONTACT D Gilbert: gilbertd@cricket.bio.indiana.edu OS Unix LANGUAGE C VOLUME - AC BC00206 NAME RESTMAP DOMAIN Restriction maps DESCRIPTION Restriction mapping programs MAPC (circular mo- DESCRIPTION lecules) and MAPL(linear molecules) DESCRIPTION In addition, an improved data entry program DESCRIPTION DIGED, is included. AUTHOR William R. Pearson RA Pearson W.R.; RT "Automatic construction of restriction site maps."; RL Nucleic Acids Res. 10:217-227(1982). RX Medline; 82150178. RX SeqAnalRef; PEAW8201. ADDRESS U. of Virginia Dept. of Biochemistry, USA. CONTACT wrp@virginia.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/restrict-enz SITE-CONTACT D Gilbert: gilbertd@cricket.bio.indiana.edu SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta = fasta(version number) SITE-CONTACT William Pearson wrp@virginia.edu OS MS-DOS , UNIX LANGUAGE FORTRAN VOLUME - COMMENTS The source code has been changed to move COMMENTS from Microsoft 3.3 to SunOSf77. COMMENTS The MAPC, MAPL, or DIGED programs and COMMENTS documentation may not be sold or incorporated COMMENTS into a commercial product, in whole or in part, COMMENTS without written consent of William R. Pearson. AC BC00369 NAME RST_OLAP DOMAIN Restriction maps DESCRIPTION Creates sorted list of restrictione enzymes DESCRIPTION giving adhesive ends from REBASE database file AUTHOR Stockwell P. 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 LANGUAGE Pascal VOLUME - AC BC00391 NAME BCM Search Launcher DOMAIN WWW server DOMAIN Sequence format conversion tools DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Structure prediction DOMAIN Pattern Identification DOMAIN Alignment Search software DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Restriction maps DOMAIN Database and analysis DOMAIN Searching databases DOMAIN Statistical significance DOMAIN Comparative analysis SERVER http://www.hgsc.bcm.tmc.edu/SearchLauncher/ DESCRIPTION The BCM Search Launcher is an integrated set of World- DESCRIPTION Wide Web (WWW) pages that organize molecular biology- DESCRIPTION related search and analysis services available on the DESCRIPTION WWW by function, and provide a single point-of-entry for DESCRIPTION related searches. The Protein Sequence Search Page, for DESCRIPTION example, provides a single sequence entry form for DESCRIPTION submitting sequences to WWW servers that provide remote DESCRIPTION access to a variety of different protein sequence search DESCRIPTION tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, DESCRIPTION PROSITE, and BLOCKS searches. Other Launch pages provide DESCRIPTION access to 1) nucleic acid sequence searches, 2) multiple DESCRIPTION and pairwise sequence alignments, 3) gene feature searches, DESCRIPTION 4) protein secondary structure prediction, and 5) DESCRIPTION miscellaneous sequence utilities (e.g., 6-frame DESCRIPTION translation). The BCM Search Launcher also provides a DESCRIPTION mechanism to extend the utility of other WWW services by DESCRIPTION adding supplementary hypertext links to results returned DESCRIPTION by remote servers. For example, links to the NCBI's DESCRIPTION Entrez database and to the Sequence Retrieval System DESCRIPTION (SRS) are added to search results returned by the NCBI's DESCRIPTION WWW BLAST server. These links provide easy access to DESCRIPTION auxiliary information, such as Medline abstracts, that DESCRIPTION can be extremely helpful when analyzing BLAST database DESCRIPTION hits. For new or infrequent users of sequence database DESCRIPTION search tools, we have pre-set the default search parameters DESCRIPTION to provide the most informative first-pass sequence DESCRIPTION analysis possible. We have also developed a batch client DESCRIPTION interface for Unix and Macintosh computers that allows DESCRIPTION multiple input sequences to be automatically searched as DESCRIPTION a background task, with the results returned as individual DESCRIPTION HTML documents directly to the user's system. AUTHOR Randall F. Smith, Brent A. Wiese, Mary K. Wojzynski, AUTHOR Daniel B. Davison , and Kim C. Worley RA Smith R.F., Wiese B.A., Wojzynski M.K., Davison D.B., Worley K.C.; RT "BCM Search Launcher--An integrated interface to molecular RT biology database search and analysis services available on RT the World-Wide Web."; RL Submitted. ADDRESS Randall F. Smith, Ph.D. ADDRESS Department of Molecular and Human Genetics, T-921, ADDRESS Baylor College of Medicine ADDRESS One Baylor Plaza, Houston, TX 77030, USA ADDRESS Tel: +1 (713) 798-4735 Fax: +1 (713) 798-5386 CONTACT rsmith@bcm.tmc.edu CONTACT kworley@bcm.tmc.edu SITE WWW Server at URL http://www.hgsc.bcm.tmc.edu/SearchLauncher/ SITE-CONTACT rsmith@bcm.tmc.edu SITE WWW Server at URL http://dot.imgen.bcm.tmc.edu:9331/downloads/software/batch_client.html SITE give information about the downloads SITE ftp anonymous dot.imgen.bcm.tmc.edu for a batch client SITE Directory /pub/software/search-launcher OS Unix and Macintosh for the batch client LANGUAGE Perl (on Unix), AppleScript (on Macintosh) VOLUME - REQUIRES MacTCP on Macintosh and AppleScript, Perl on Unix 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 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 BC00566 NAME CloneIt DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Restriction maps DESCRIPTION Molecular biologists often have to sub-clone DESCRIPTION plasmidic vectors: a DNA plasmid is cleaved and ligated DESCRIPTION with an exogen DNA fragment previously excised from an DESCRIPTION other plasmid. The necessary cuts are made by restriction DESCRIPTION enzymes which then must be carefully choosen in order to DESCRIPTION minimize the steps required to obtain the desired DESCRIPTION molecule. During the selection of those enzymes, the main DESCRIPTION difficulties encountered come from the knowldege of: DESCRIPTION the enzymes' characteristics DESCRIPTION the localization of the cuts within the sequence DESCRIPTION the complementarity between the protuding ends DESCRIPTION the possible self ligation of the vector DESCRIPTION the use of modifying DNA polymerases that generate blunt ends DESCRIPTION the constraint to clone the insert in-frame with a vector sequence DESCRIPTION the use of partial digestions DESCRIPTION the creation of a stop codon after the ligation. DESCRIPTION This exercise takes a long time even with a DESCRIPTION computorized help of the classic DNA analysis softwares, DESCRIPTION such as "DNA Strider" , that only help the user by DESCRIPTION localizing restriction sites that are present a few times DESCRIPTION in a plasmid sequence. All combinations cannot be humanly DESCRIPTION checked by the scientist, so a simple cloning strategy can DESCRIPTION be missed by the experimenter. DESCRIPTION The program is not an expert system, as it does not "learn" DESCRIPTION the logical steps accomplished by the biologist and it does DESCRIPTION not have to be accompanied in its search: it just runs an DESCRIPTION algorithm that explores all the possible enzymes DESCRIPTION combinations that could be used to clone the molecules. DESCRIPTION This program called CloneIt , written in ANSI C, provides a DESCRIPTION useful aid for any molecular biologist who wants to quickly DESCRIPTION find sub-cloning, in-frame deletions, frameshifts DESCRIPTION strategies, which would otherwise be difficult to DESCRIPTION discover. This program handle parameters such as DESCRIPTION usage of a phosphatase (CIP) DESCRIPTION usage of modifying polymerases that blunt overhanged ends DESCRIPTION partial digestions DESCRIPTION 5' or/and 3' in-frame ligation DESCRIPTION digestion post ligation DESCRIPTION digestion to direct insert DESCRIPTION detection of stop codon after ligation DESCRIPTION Compare 2 sequences from the point of view of restriction sites. DESCRIPTION Display a restriction map. DESCRIPTION Translation of restriction enzymes databases. DESCRIPTION Management of large cloning projects. AUTHOR Pierre LINDENBAUM RA Lindenbaum P.; RT "CloneIt: finding cloning strategies, in-frame deletions and RT frameshifts."; RL Bioinformatics 14(5):465-466(1998). ADDRESS Pierre LINDENBAUM. ADDRESS Laboratoire de Biologie Moleculaire des Rotavirus. ADDRESS Virologie et Immunologie Moleculaires. ADDRESS Institut National de la Recherche Agronomique. ADDRESS 78350 Jouy-en-Josas Cedex FRANCE. CONTACT lindenb@biotec.jouy.inra.fr SITE WWW Server at URL http://locus.jouy.inra.fr/soft/cloneit/cloneit.html OS UNIX, MAC, PC LANGUAGE ANSI-C VOLUME about 200 Ko REQUIRES C compilator (works with GCC) COMMENTS I would like to thank Audrey Nepveu-de-Villemarceau, COMMENTS Janine L., Dr S. Hazout and his team, Philippe Bessieres, COMMENTS Christine Young, and Maria Piron for their help. AC BC00571 NAME Redasoft Plasmid 1.0 DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Genetic and Physical Mapping DOMAIN Restriction maps DESCRIPTION Redasoft Plasmid 1.0 is an exciting new software tool DESCRIPTION designed to to help life scientists draw high quality DESCRIPTION (circular or linear) vector maps (with or without sequence) DESCRIPTION and perform DNA sequence analysis quickly and easily. DESCRIPTION DESCRIPTION Plasmid includes revolutionary new features such as an DESCRIPTION integrated web browser and the ability to automatically DESCRIPTION parse Genbank and EMBL / VectorDB files and display them as DESCRIPTION fully labeled graphical maps! DESCRIPTION DESCRIPTION Plasmid includes a database of nearly 1000 enzymes, support DESCRIPTION for multiple swquence file formats and a custom restriction DESCRIPTION enzyme list. AUTHOR Redasoft RT - ADDRESS - CONTACT info@redasoft.com SITE WWW Server at URL http://www.redasoft.com OS Windows 95/98/NT LANGUAGE C++ VOLUME 2 MB REQUIRES - AC BC00583 NAME CloneIt Online DOMAIN Sequence tools DOMAIN Pattern Identification DOMAIN Restriction maps DOMAIN WWW server SERVER http://topaze.jouy.inra.fr DESCRIPTION Molecular biologists often have to sub-clone plasmidic DESCRIPTION vectors: a DNA plasmid is and ligated with an exogen DNA DESCRIPTION fragment previously excised from an other plasmid. The DESCRIPTION necessary cuts are achieved by restriction enzymes which DESCRIPTION then must be carefully choosen in order to minimize the DESCRIPTION steps required to obtain the desired molecule. During the DESCRIPTION selection of those enzymes, the main difficulties DESCRIPTION encountered come from: the knowldege of: DESCRIPTION the enzymes' characteristics DESCRIPTION the localization of the cuts within the sequence DESCRIPTION the complementarity between the protuding ends DESCRIPTION the possible self ligation of the vector DESCRIPTION the use of modifying DNA polymerases generating blunt ends DESCRIPTION the constraint to clone the insert in-frame with a vector sequence DESCRIPTION the use of partial digestions DESCRIPTION the creation of a stop codon after the ligation. DESCRIPTION We developed the CloneIt program that quickly finds DESCRIPTION in-frame deletions using restriction enzymes and DESCRIPTION frameshifts (using digestion, fill-in and ligation) in a DESCRIPTION plasmid sequence, Then, as the main functions and DESCRIPTION procedures were being developed, we have extended the DESCRIPTION capacities of the program to find strategies to sub-clone a DESCRIPTION fragment from a plasmid to another vector while still DESCRIPTION controling the problems described above. This program is DESCRIPTION not an expert system, as it does not "learn" the logical DESCRIPTION steps accomplished by the biologist and it does not have to DESCRIPTION be accompanied in its search: it just runs an algorithm DESCRIPTION that explores all the possible enzymes combinations that DESCRIPTION could be used to clone the molecules. DESCRIPTION This program provides a useful aid for any molecular DESCRIPTION biologist who wants to quickly find sub-cloning, in-frame DESCRIPTION deletions, frameshifts strategies, which would otherwise be DESCRIPTION difficult to discover. AUTHOR Pierre LINDENBAUM, Christophe CARON RA Lindenbaum P.; RT "CloneIt: finding cloning strategies, in-frame deletions and frameshifts."; RL Bioinformatics 14(5):465-466(1998). ADDRESS Pierre LINDENBAUM. ADDRESS Laboratoire de Biologie Moleculaire des Rotavirus. ADDRESS Virologie et Immunologie Moleculaires. ADDRESS Institut National de la Recherche Agronomique. ADDRESS 78350 Jouy-en-Josas Cedex FRANCE. ADDRESS lindenb@biotec.jouy.inra.fr CONTACT lindenb@biotec.jouy.inra.fr SITE WWW Server at URL http://topaze.jouy.inra.fr/cgi-bin/CloneIt/CloneIt OS - LANGUAGE - VOLUME - REQUIRES - COMMENTS Merci a Mademoiselle DERAT pour son aide. 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 -