Catalogue of Molecular Biology Programs Release 5.6 27 Jan 1998 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00052 NAME GMD DOMAIN Genetic and Physical Mapping DESCRIPTION Programs to assist in the design of genome DESCRIPTION mapping experiments (contig mapping) AUTHOR Fu Y. and Arnold J. RA Fu Y.-X., Timberlake W.E., Arnold J.; (1992). RT "On the design of genome mapping experiments RT using short synthetic oligonucleotides"; RL Biometrics 48:337-359(1992). RX Medline; 92345531. ADDRESS Center for Demographic and Population Genetics, ADDRESS University of Texas, Houston 77225. USA. CONTACT arnold@bcsf.uga.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 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/unix SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS Unix, VAX/VMS LANGUAGE - VOLUME - AC BC00370 NAME GMENDEL DOMAIN Genetic and Physical Mapping DESCRIPTION program to facilitate genetic mapping. A coding system is used DESCRIPTION in the program that enables it to handle a broad range of data. DESCRIPTION We have put likelihood functions for commonly used mapping DESCRIPTION populations in a default database (dfefreq.data) and likelihood DESCRIPTION functions for mapping populations of mating between heterozygous DESCRIPTION parents in a complex database Prediction of membran protein DESCRIPTION structure . Users can create likelihood functions for their DESCRIPTION specific problems and put them into the data bases by following DESCRIPTION the coding system. AUTHOR - RT - ADDRESS - CONTACT - SITE - SITE-CONTACT - OS UNIX system with at least 8 MB memory LANGUAGE - VOLUME - AC BC00371 NAME GenomeView DOMAIN Genetic and Physical Mapping DESCRIPTION GenomeView is an environement for human genome maps construction DESCRIPTION and data browsing. It is built on top of the OODBMS IDB. DESCRIPTION It is available trough a mail-server,a WWW server AUTHOR Viara E., Pook S., Lacroix B., Tissot M., Atlan L., AUTHOR Cohen-Akenine A., Vaysseix G., E. Barillot E.; RA Viara E., Pook S., Lacroix B., Tissot M., Atlan L., RA Cohen-Akenine A., Vaysseix G., E. Barillot E.; RT "The IDB database system and its use in the human RT genome project: HUGEMAP."; RL Interconnection of Molecular Biology Databases, RL Stanford, California, 1994. AB This paper is available at the following AB URL http://www.genethon.fr/confs/mimdb_abs.html ADDRESS Genethon, 13 place de Rungis, 75013 Paris, FRANCE CONTACT Emmanuel.Barillot@infobiogen.fr SITE WWW Server at URL http://ceph-genethon-map.genethon.fr/ceph-genethon-map.html OS Solaris 2.3 LANGUAGE C,C++ VOLUME - AC BC00372 NAME ICRF_CONTIG DOMAIN Genetic and Physical Mapping DESCRIPTION The ICRF contig-building package is a DESCRIPTION suite of programs to aid the construction of DESCRIPTION physical maps from hybridisation data AUTHOR Mott R.F. and Grigoriev A.V. RA Mott R.F., Grigoriev A., Maier E., Hoheisel J., Lehrach H.; RT "Algorithms and software tools for ordering clone libraries: RT application to the mapping of the genome of RT Schizosaccharomyces pombe."; RL Nucleic Acids Res. 21:1965-1974(1993). RX Medline; 93261833. RX SeqAnalRef; MOTR9301. RA Grigoriev A., Mott R., Lehrach H.; RT "An algorithm to detect chimeric clones and random noise RT in genomic mapping."; RL Genomics 22:482-486(1994). ADDRESS Genome Analysis Laboratory, Imperial Cancer Reserach Fund ADDRESS 44 Lincoln's Inn Fields ADDRESS Londons WC2A 3PX, UK CONTACT rmott@gea.lif.icnet.uk - andy@gea.lif.icnet.uk 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 OS Unix LANGUAGE C, Xview VOLUME - AC BC00373 NAME ODS DOMAIN Genetic and Physical Mapping DESCRIPTION Programs are now available to assist in the in DESCRIPTION vitro reconstruction of chromosomes or DESCRIPTION chromosome fragments ("contig mapping") DESCRIPTION from a clonal library. DESCRIPTION ODS is a program that orders DNA sequences DESCRIPTION based on similarity of their binary profiles DESCRIPTION assigned to clones in a library by one of DESCRIPTION several experimental approaches. AUTHOR A. Jamie Cuticchia RT Cuticchia, A.J., Arnold, J., and W.E. RT Timberlake (1993). "ODS: Ordering DNA RT Sequences, a physical mapping algorithm based RT on simulated annealing". CABIOS, 9(2),215-219. RT Cuticchia, A.J., J. Arnold, and W.E. Timberlake (1992). RT The use of simulated annealing in chromosome reconstruction RT experiments based on binary scoring. Genetics 132: 591-601 RT Wang, Y., Prade, R. A., Griffith, J., Timberlake, W.E., RT and Arnold, J. (1994) A fast random cost algorithm RT for physical mapping. PNAS, 91, 11094-11098 RA Cuticchia A.J., Arnold J., Timberlake W.E.; RT " Physical Mapping Algorithm Based on Simulated Annealing."; RL Comput. Appl. Biosci. 9(2):215-219 (1993). ADDRESS Genetics Department, University of Georgia, Athens, GA 30602, USA CONTACT arnold@bscr.uga.edu SITE - SITE-CONTACT - OS VAX/VMS operating system The OS programs have been run with minor modification OS on VAXstations,a DECstation 3100, and on a OS Silicon Graphics IRIS 4D70/GT workstation. LANGUAGE FORTRAN, C VOLUME - COMMENT The programs also have been incorporated into COMMENT a DNA sequence analysis package (Arnold et al., COMMENT 1986), and can be accessed directly on the COMMENT Biological Sequence/Structure Computational COMMENT Facility (BS/SCF). Contact Dr. Weise for a COMMENT guest account at: WEISE@BSCF.UGA.EDU AC BC00374 NAME ODS_BOOTSTRAP DOMAIN Genetic and Physical Mapping DESCRIPTION Assesses the reliability of physical maps by bootstrap resampling AUTHOR Y. Wang, R.A. Prade, J. Griffith, W.E. Timberlake RA Wang Y., Prade R.A., Griffith J., Timberlake W.E., Arnold, J.; RT "ODS_BooTstrap: assessing the statistical RT reliability of physical maps by bootstrap resampling."; RL Comput. Appl. Biosci. 10(6):625-634(1994). RX SeqAnalRef; WANY9401. ADDRESS Genetics Department, University of Georgia, Athens, GA 30602,USA CONTACT arnold@bscr.uga.edu SITE - SITE-CONTACT arnold@bscr.uga.edu OS VAX/VMS LANGUAGE C VOLUME - AC BC00375 NAME QUICKMAP DOMAIN Genetic and Physical Mapping DESCRIPTION A compact database and navigation tool for the physical map DESCRIPTION of the human genome. AUTHOR P. Rigault and E. Poullier RT - ADDRESS Fondation Jean Dausset CEPH ADDRESS 27, rue Juliette Dodu,75010 Paris,France CONTACT P. Rigault: rigault@cephb.fr SITE ftp anonymous ceph-genethon-map.cephb.fr SITE Directory /pub/ceph-genethon-map/QUICKMAP SITE_CONTACT E. Poullier: poullier@cephb.fr OS Sun OS with X11R4 or X11R5 LANGUAGE C, VOLUME - COMMENTS Binary distribution for Sun OS. COMMENTS Can work on Solaris 2 through binary compatibility package. AC BC00376 NAME SIGMA DOMAIN Genetic and Physical Mapping DESCRIPTION System for Integrated Genome Map Assembly DESCRIPTION graphical genome map editor DESCRIPTION As a viewer, Sigma puts full color maps of the genome in DESCRIPTION the users hands to display, browse, manipulate, and print. DESCRIPTION It is capable of giving the user a perspective on an entire DESCRIPTION chromosome map, as well as an arbitrarily detailed view. In DESCRIPTION fact, it can do both at the same time. A number of DESCRIPTION features allow the user to easily find whatever specific DESCRIPTION part of a map he or she wishes to view, as well as browse DESCRIPTION openly through the map. In short, it is an extremely DESCRIPTION flexible tool, one that is accommodating to a variety of DESCRIPTION viewing styles and objectives. DESCRIPTION As a map editor, Sigma allows the user to integrate data DESCRIPTION from a variety of sources into a single map, which can then DESCRIPTION be evaluated as a whole. A convenient user interface makes DESCRIPTION data entry easy, and a collection of powerful features DESCRIPTION simplify elaborate and complicated editing tasks. AUTHOR Theoretical Biology and Biophysics Group (T-10) at Los Alamos AUTHOR National Laboratory (LANL), Los Alamos RT - ADDRESS Los Alamos National Laboratory (LANL), Los Alamos CONTACT - SITE ftp anonymous ftp.ncgr.org SITE Directory /pub/sigma SITE-CONTACT sigma@ncgr.org SITE http://www.ncgr.org/sigma/home.html SITE-CONTACT sigma@ncgr.org SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/linkage_and_mapping/SIGMA SITE-CONTACT nethelp@ebi.ac.uk OS Sun SparcStation (as a Motif application), Mac OS, Dec Alpha LANGUAGE C VOLUME - AC BC00380 NAME CEPHViewer DOMAIN Genetic and Physical Mapping DESCRIPTION CEPHViewer is a client-server database to browse and DESCRIPTION manipulate CEPH mapping data. It assists viewing the DESCRIPTION large volume of data from physical and genetic mapping. DESCRIPTION It takes the CEPH physical data and can include DESCRIPTION independant data. The server is build using Sybase RDBMS DESCRIPTION on the unix side and the client is built on a macintosh DESCRIPTION using 4D. AUTHOR P.M. Nadkarni, P. Bray-Word RA Nadkarni P.M., Bray-Word P.; RT "CEPHViewer: a client-server database to browse RT CEPH physical mapping and linkage data."; RL Genomics 25:318-320(1995). ADDRESS Center for Medicals Informatics and Dept of Genetics ADDRESS Yale University School of Medecine ADDRESS New Haven, Connecticut 06510, USA. CONTACT - SITE - SITE-CONTACT - OS Unix & Macintosh LANGUAGE - VOLUME - REQUIRES Sybase licence on Unix, 4D licence on Macintosh COMMENTS Contact the authors to get the programs and database definition AC BC00413 NAME CONTIG DOMAIN Genetic and Physical Mapping DESCRIPTION A genome mapping package has been developed for reading and DESCRIPTION assembling data from clones analysed by restriction enzyme DESCRIPTION fragmentation and polyacrylamide gel electrophoresis. The DESCRIPTION package comprises: data entry; matching; assembly; statistical DESCRIPTION analysis; modelling. The Data is entered by a scanning and image DESCRIPTION processing system, called IMAGE. The primary emphasis in the DESCRIPTION analytical routines is on flexibility DESCRIPTION and interactive convenience, so that the operator has DESCRIPTION full knowledge of and control over the growing map, DESCRIPTION but a variety of automatic options are included. The DESCRIPTION package continually grows to meet the needs of the DESCRIPTION Caenorhabditis project. DESCRIPTION It is the Unix port of CONTIG9 genome database software. AUTHOR Sanger Centre RA Sulston J., Mallett F., Staden R., Durbin R., Horsnell T., Coulson A.; RT "Software for genome mapping by fingerprinting techniques."; RL Comput. Appl. Biosc. 4(1):125-132(1988). RX Medline; 88252874. ADDRESS Sanger Centre ADDRESS Hinxton Hall, Hinxton, Cambs CB10 1RQ, UK CONTACT fw@sanger.ac.uk SITE ftp anonymous ftp.sanger.ac.uk SITE Directory /pub/contigc/ SITE-CONTACT fw@sanger.ac.uk SITE WWW Server at URL http://www.sanger.ac.uk/~fw/ContigC/index.html OS Unix LANGUAGE ANSI-C VOLUME - REQUIRES ANSI-C compiler AC BC00437 NAME MIM DOMAIN Genetic Linkage software DOMAIN Genetic and Physical Mapping DOMAIN Statistical significance DOMAIN Multivariate analysis DESCRIPTION MIM is a program to implement the Multipoint IBD method for DESCRIPTION partitioning genetic variance of quantitative traits to DESCRIPTION specific chromosomal regions using data on nuclear families. AUTHOR David E. Goldgar, Cathryn M. Lewis, Khosrow Gholami, AUTHOR Edward N. Kort RA Goldgar D.E.; RT "Multipoint analysis of human quantitative genetic variation."; RL Am. J. Hum. Genet. 45:957-967(1990). RA Goldgar D.E., Oniki R.O.; RT "Comparison of a multipoint identity by descent method with RT parametric multipoint linkage analysis for mapping quantitative traits."; RL Am. J. Hum. Genet. 50:598-606(1992). ADDRESS Cathryn Lewis, Ph.D. ADDRESS Genetic Epidemiology ADDRESS 391 Chipeta Way, D2 ADDRESS Salt Lake City, UT 84108, USA CONTACT edward@episun2.med.utah.edu SITE ftp anonymous morgan.med.utah.edu SITE Directory /pub/Mim SITE-CONTACT - OS UNIX LANGUAGE C VOLUME 250K bytes REQUIRES - COMMENTS Copies of the program may be obtained COMMENTS by contacting Edward Kort at edward@episun2.med.utah.edu AC BC00439 NAME RHMAP DOMAIN Genetic and Physical Mapping DESCRIPTION RHMAP is a program package for the DESCRIPTION statistical analysis of radiation hybrid mapping data AUTHOR Michael Boehnke RT - ADDRESS Department of Biostatistics, ADDRESS University of Michigan, ADDRESS USA CONTACT boehnke@umich.edu SITE WWW Server at URL http://www.sph.umich.edu/group/statgen/software SITE-CONTACT boehnke@umich.edu SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/linkage_and_mapping/RHMAP_SIMLINK SITE-CONTACT nethelp@ebi.ac.uk OS UNIX and DOS LANGUAGE FORTRAN 77 VOLUME - REQUIRES - AC BC00442 NAME DISLAMB, DISMULT DOMAIN Genetic tools DOMAIN Genetic and Physical Mapping DOMAIN Genetic Linkage software DESCRIPTION Linkage Disequilibrium Analysis DESCRIPTION There are four programs included DESCRIPTION 1) DISLAMB for single locus linkage disequilibrium analysis DESCRIPTION for a multiallelic system DESCRIPTION 2) DISMULT for multilocus linkage disequilibrium analysis DESCRIPTION 3) TDTLIKE for multiallelic likelihood-based version of the DESCRIPTION TDT test for linkage in pedigree material. DESCRIPTION 4) MCNMULT for multilocus-multiallelic likelihood-based DESCRIPTION version of the McNemar test for linkage disequilibrium in DESCRIPTION pedigree material. DESCRIPTION DISLAMB and DISMULT are discribed in the documentation file DESCRIPTION diseq.doc, and TDTLIKE and MCNMULT are described in the DESCRIPTION file tdtlike.doc AUTHOR J.D. Terwilliger RA Terwilliger J.D. RT "A Powerful Likelihood Method for the Analysis of Linkage RT Disequilibrium Between Trait Loci and One or More RT Polymorphic Marker Loci."; RL Am. J. Hum. Genet. 56:777-787(1995). ADDRESS Wellcome Trust Center for Human Genetics ADDRESS Windmill Road ADDRESS Headington OX3 7BN Oxford, UK CONTACT joe@well.ox.ac.uk SITE ftp anonymous ftp.well.ox.ac.uk SITE Directory /pub/software/diseq SITE-CONTACT joe@well.ox.ac.uk SITE ftp anonymous linkage.rockefeller.edu SITE Directory /software/diseq SITE-CONTACT wli@linkage.rockefeller.edu SITE WWW Server at URL http://linkage.rockefeller.edu/ OS Solaris, SunOS, OSF/1, VMS LANGUAGE PASCAL VOLUME - REQUIRES PASCAL Compiler AC BC00446 NAME CROSSFIND DOMAIN Genetic and Physical Mapping DOMAIN Genetic tools DESCRIPTION Package to analyse CRI-Map chrompic output and detect well- DESCRIPTION supported breakpoints in CEPH family data. Can produce multi- DESCRIPTION page PostScript diagrams of the breakpoints. AUTHOR J. Attwood, S. Povey RT Submitted Annals of Human Genetics, Oct 95 ADDRESS MRC Human Biochemical Genetics Unit ADDRESS University College London ADDRESS Wolfson House, 4 Stephenson Way ADDRESS London NW1 2HE, UK CONTACT john@galton.ucl.ac.uk SITE ftp anonymous ftp.gene.ucl.ac.uk SITE Directory /pub/packages/jattwood SITE-CONTACT help@galton.ucl.ac.uk SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/linkage_and_mapping/gene_ucl_uk SITE-CONTACT nethelp@ebi.ac.uk OS Unix, MSDOS LANGUAGE C, PostScript VOLUME - REQUIRES CRI-Map v2.4 AC BC00449 NAME GRAM DOMAIN Genetic and Physical Mapping DESCRIPTION GRAM (Genomic Restriction Map Assembly) takes as input single DESCRIPTION digest data from a set of overlapping clones and produces one or DESCRIPTION more plausible partially ordered restriction maps along with the DESCRIPTION alignment of the clones. Due to the error and uncertainty in the DESCRIPTION data, the exact solution cannot generally be calculated; DESCRIPTION therefore, GRAM provides interactive graphics so that the user DESCRIPTION can detect and fix the error. The GRAM Editor allows the user to DESCRIPTION view the fragments of a clone and to add, delete, and modify DESCRIPTION fragments. The Clone Manager allows the user to add and delete DESCRIPTION clones from the input set; it also has list processing DESCRIPTION capabilities so that sub-contigs can be built and combined. DESCRIPTION Additional features allow the user to specify that two clones do DESCRIPTION or do not overlap, or that two fragments are or are not the DESCRIPTION same. The end fragments are ignored during the initial assembly DESCRIPTION and display of a contig, but the user can request that the end DESCRIPTION fragments be fitted to a contig. AUTHOR Soderlund C., Burks C. RA Soderlund C., Burks C.; RT "GRAM and genfragII: solving and testing the single-digest, partially RT ordered restriction map problem."; RL Comput. Appl. Biosci. 10(3):349-358(1994). RX Medline; 95007046. RX SeqAnalRef; SODC9401. ADDRESS Center for Human Genome Studies, ADDRESS Los Alamos National laboratory, ADDRESS Los Alamos NM 87545, USA CONTACT cari@sanger.ac.uk SITE ftp anonymous atlas.lanl.gov SITE Directory /pub/gram SITE-CONTACT - SITE WWW Server at URL http://www-ls.lanl.gov/gram_source.html SITE-CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/linkage_and_mapping/sanger_uk SITE-CONTACT nethelp@ebi.ac.uk OS SunOS and Solaris LANGUAGE C VOLUME - REQUIRES - AC BC00451 NAME SAM DOMAIN Genetic and Physical Mapping DESCRIPTION SAM (System for Assembling Markers) takes an input a file of DESCRIPTION marker hybridization (or marker content) results for a set of DESCRIPTION clones. Via a SAM function, the markers can be ordered; the DESCRIPTION output is a graphical display which shows the order of the DESCRIPTION markers and the alignment of the clones to the markers. The DESCRIPTION clones can then be ordered based on the map. The solution can be DESCRIPTION saved in a file which can subsequently be loaded back into SAM. DESCRIPTION The Clone Manager allows the user to pick subsets of clones to DESCRIPTION assemble; or the user can request SAM to find a set of clones DESCRIPTION which contain one or more markers. The Clone Editor allows the DESCRIPTION user to add, delete and modify clone hybridization results DESCRIPTION (called Cmarks for Clone Markers). The user can also edit the DESCRIPTION SAM display by moving clones or markers. DESCRIPTION There can be different types of markers where each type is DESCRIPTION represented by a number and a color. For the Chromosome 22 data, DESCRIPTION we use the following types: Probe 1 Turquoise, Sts 2 Green, End DESCRIPTION 3 Yellow, Other 4 Beige, Repeat 5 Rose, Alu-PCR 6 Brown. The DESCRIPTION last two types are not discrete which can result in a poor DESCRIPTION marker map; therefore, SAM has functions to exclude a marker DESCRIPTION type, and then allows the user to specify markers from that type DESCRIPTION which should not be excluded. Excluded markers can be displayed DESCRIPTION to the right of the map. DESCRIPTION SAM was derived from GRAM which takes as input single digest DESCRIPTION data from a set of overlapping clones and produces one or more DESCRIPTION plausible partially ordered restriction maps along with the DESCRIPTION alignment of the clones. DESCRIPTION GRAM Biocat Acc: BC00449 AUTHOR Cari Soderlund RA Soderlund C., Dunham I.; RT "SAM: a system for iteratively building marker maps."; RL Comput. Appls. Biosci. 11(6):645-655(1995). ADDRESS Sanger Centre, ADDRESS Hinxton Hall, Hinxton, Cambs CB10 1RQ, UK CONTACT cari@sanger.ac.uk SITE ftp anonymous ftp.sanger.ac.uk SITE Directory /pub/sam SITE-CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/linkage_and_mapping/sanger_uk SITE-CONTACT nethelp@ebi.ac.uk SITE WWW Server at URL http://www.sanger.ac.uk/~cari/sam.html OS UNIX (SunOS, Solaris, OSF1, SGI) LANGUAGE C VOLUME - REQUIRES - AC BC00499 NAME FPC (FingerPrinted Contigs) DOMAIN Genetic and Physical Mapping DESCRIPTION FPC aids the user in creating fingerprinted contigs. DESCRIPTION The program has both automatic routines and interactive DESCRIPTION graphics to support contig building. DESCRIPTION It takes as input a set of clones and their restriction DESCRIPTION fragments (called Bands); here at the Sanger Centre we DESCRIPTION use the program called Image to produce our bands files. DESCRIPTION Marker data is supported. DESCRIPTION FPC uses the ACeDB graphics library. DESCRIPTION FPC replaces contig9. AUTHOR C. Soderlund, I. Longden ADDRESS The Sanger Centre ADDRESS Hinxton Hall ADDRESS Cambridge, CB10 1SA, UK CONTACT cari@sanger.ac.uk SITE ftp anonymous ftp.sanger.ac.uk SITE Directory /pub/fpc OS Unix LANGUAGE C VOLUME - REQUIRES - COMMENTS The ftp directory for FPC contains executables for COMMENTS Dec Alpha, SUN, SGI and Linux. It also contains a demo.tar COMMENTS file and a poscript manual. COMMENTS The source code can be obtained upon request. AC BC00513 NAME Grouper DOMAIN Genetic tools DOMAIN Genetic and Physical Mapping DESCRIPTION Grouper creates sets of non-overlapping microsatellite markers DESCRIPTION for high-throughput multiplex genotyping eperiments. DESCRIPTION Efficient high-throughput genotyping experiments DESCRIPTION require the multiplexing of polymorphicmarkers, i.e. DESCRIPTION the use of multiple markers with non-overlapping allele size DESCRIPTION ranges in a single lane of a genotyping gel. Grouper assists DESCRIPTION in the arrangement of such markers into sets. AUTHOR Rainer Fuchs ADDRESS Glaxo Wellcome Research and Development ADDRESS 5 Moore Drive ADDRESS Research Triangle Park, NC 27709 ADDRESS USA CONTACT rainer_fuchs@glaxowellcome.com SITE ftp anonymous ftp.ebi.ac.uk SITE Directory pub/software/unix SITE-CONTACT nethelp@ebi.ac.uk OS UNIX LANGUAGE C VOLUME 150 K REQUIRES -