HUM-MOLGEN archive: Linkage Newsletter

Linkage Newsletter Vol. 9 No. 3 November 1995 Published by Jurg Ott, Columbia University, New York Email: jurg.ott@columbia.edu WWW: http://linkage.cpmc.columbia.edu Postal address: Columbia University, Unit 58 722 West 168 Street New York, NY 10032 Editorial Assistant: Katherine Montague Email: km165@columbia.edu or kath@linkage.cpmc.columbia.edu Fax: 212-568-2750 Tel: 212-960-2507 LINKAGE COURSES The next four linkage courses have been scheduled as fol- lows: January 8-12, 1996, at Columbia University, New York (ad- vanced course, maximum of 20 participants, deadline for applica- tion is Nov. 10). February 26 - March 1, 1996, at the University of Zurich, Irchel Campus Computer Center, Switzerland (basic course, maximum of 18 participants). June 10-14, 1996, at Columbia University, New York (basic course, maximum of 30 participants). June 24-28, 1996, at Columbia University, New York (basic course, maximum of 30 participants). To obtain information on these courses, please write to Katherine Montague, course coordinator, by email (preferred) or fax. We will use our book (Terwilliger and Ott, "Handbook of Human Genetic Linkage," Johns Hopkins University Press, 1994), with supplemental handouts for advanced courses. Participants are expected to buy the book and bring it to the course; in case of problems please contact Katherine Montague in advance of the course. A list of corrections for the book may be downloaded from our anonymous ftp site, linkage.cpmc.columbia.edu (file corr_ter.txt in directory book). SOFTWARE NEWS Bug in FastLINK Rita Kruse, Bonn Germany, made me aware of the following problem in FastLINK: For a pedigree with seven loops, the lod score was different depending on the order in which "loop individuals" were defined. For one order, a maximum lod score of 6.50 was obtained while under another order, with the same data, the maximum lod score was only 0.66. This difference occurred only with FASTLINK while the LINKAGE programs consistently furnished a lod score of 6.50. Dr. Alejandro Schaffer confirmed this bug and has already corrected it in version 2.3P of FASTLINK. SIMLINK and RHMAP on the Web The following announcement was contributed by Dr. Michael Boehn- ke, Ann Arbor: For some time, I have been distributing two programs for genetic analysis: RHMAP and SIMLINK. RHMAP is a program package for the statistical analysis of radiation hybrid mapping data. SIMLINK is a program for evaluating the statistical power of a proposed linkage study. Both RHMAP and SIMLINK are written in FORTRAN 77, and both previously were distributed free of charge on floppy diskettes after completion of a user agreement. Beginning October 31, 1995, the primary method of distribution for RHMAP and SIMLINK will be via the World Wide Web (WWW). To access the current versions of RHMAP and SIMLINK (2.01 and 4.11, respectively), you will need a WWW browser such as Mosaic or Netscape. Using a browser, you can download the software packag- es from http://www.sph.umich.edu/group/statgen/software. Both analysis packages, containing source code and manuals, are available as archives for Unix and DOS systems. Once you down- load the program package archives, you will need to dearchive the files. On Unix computers the "tar" utility should be used, e.g., "tar -xvf filename". (For other computer systems, e.g., VMS, etc., one can usually obtain public-domain utilities which can read "tar" files. Links to several such utilities are provided on the web page.) Simply compile the FORTRAN 77 code on your computer to obtain an executable. For DOS computers the archives are self-extracting and contain DOS executables of the programs. Simply issue the name of the archive as a DOS command, e.g., rhmapzip.exe, and all the files in the package, including the executable(s), will be extracted. Also beginning October 31, the primary method for notification of software updates for RHMAP and SIMLINK will be via e-mail. If you already have or do in the future obtain one or both of the programs, I urge you to add yourself to the appropriate mailing list by sending a short e-mail note to me at boehnke@umich.edu indicating which package(s) you use and your preferred e-mail address for notification. This will insure that you continue to get program updates, and will be helpful for me at grant renewal time. For those who lack Internet access, I will continue to distribute RHMAP and SIMLINK by floppy diskette. However, I ask you to make use of this option only if it truly is necessary. In this case, you will need to request a user agreement which you will need to fill out and send back. Please feel free to contact me if you have any questions. ----------------------------------------------------------------- Michael Boehnke Phone: 313-936-1001 Department of Biostatistics FAX: 313-763-2215 University of Michigan E-Mail: boehnke@umich.edu ----------------------------------------------------------------- Announcement of GenoCheck program The following announcement was contributed by Dr. Margaret Gelder Ehm, Houston: GenoCheck, version 1.0 Meg Gelder Ehm Rice University Department of Statistics Houston, Texas USA gelder@stat.rice.edu New error detection capabilities are available for genetic linkage data! GenoCheck, 1.0 is an error checking program designed to identify individuals and loci that are likely to contain errors. The statistical method was designed to identify typing error, but is general enough to pinpoint any unlikely genotype still consistent with Mendelian inheritance. GenoCheck was developed using FASTLINK 2.2 (modified version of LINKAGE 5.1) and uses a similar file configuration and installa- tion procedure. The code contains checkpointing facilities that allow users to recover from crashes without having to rerun the program and comes with documentation. The instructions for retrieving the code are given below: ftp softlib.cs.rice.edu Login as anonymous and leave your full e-mail address as the password. cd pub/GenoCheck In that directory you will find various files. You can get everything at once by retrieving: genocheck.tar.Z and then (outside of ftp) doing the commands: uncompress genocheck.tar.Z tar xvf genocheck.tar If you prefer to get the files piecemeal, instead of getting genocheck.tar.Z start by getting README*. The file README (with no extension) will describe all of the documentation. The statistical algorithm implemented in GenoCheck, version 1.0 is described in the papers: M. G. Ehm, R. W. Cottingham Jr., and M. Kimmel. Error Detection in Genetic Linkage Data Using Likelihood Based Methods. Journal of Biological Systems, Vol. 3, No. 1 (1995) 13-25. M. G. Ehm, R. W. Cottingham Jr., and M. Kimmel. Error Detection in Genetic Linkage Data Using Likelihood Based Methods. American Journal of Human Genetics, Vol. 58, No. 1 (1996) (to appear). Please e-mail any questions or suggestions about GenoCheck to gelder@stat.rice.edu. INFOBIOGEN server on the Web Dr. Lucien Bachner (bachner@infobiogen.fr) requested that information about his server be included in this newsletter. Here is a brief description: The server may be accessed at URL http://www.infobiogen.fr/vjf/server_vjf.html. Academic users may obtain an account at Infobiogen (after returning a form) which enables them to access a large number of programs and databases useful for gene mapping and DNA analysis. Interaction with the server is in French. Dr. Bachner is also organizing linkage training courses at the beginners level. The first was held October 24-25, he is planning the second for end of May 96 or June. Language is French. The same course is also scheduled at Institut Pasteur, December 19-20. New version of ANALYZE package A new version of the ANALYZE program package has been released. It simplifies the performance of a large array of parametric and nonparametric tests for linkage and association on data entered in LINKAGE format pedigree and parameter files. The programs are distributed at two different sites. You can obtain them either from ftp.well.ox.ac.uk in directory software/analyze or from linkage.cpmc.columbia.edu in directory software/analyze. Users are advised to download and study the README files. A DOS version of the whole package is in preparation and should be available on the latter ftp site by the end of November. SURVEY We occasionally hear from people that they are having problems obtaining our books through book stores. Typically these books are not stocked in regular book stores but those outlets designated by the Johns Hopkins University Press should always have books on stock. Readers who had problems obtaining our books (either through a book store or directly from the publisher) are invited to let us know; please also indicate the date when you had problems. We would like to have customer service improved in this area. Support through grant HG00008 from the National Center for Human Genome Research is gratefully acknowledged.