From owner-gene-linkage@net.bio.net Fri Mar 01 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!gatech!newsfeed.internetmci.com!in2.uu.net!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: bhade@aol.com (BHade) Newsgroups: bionet.molbio.gene-linkage Subject: genetic inheritance Date: 1 Mar 1996 22:34:33 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 2 Sender: root@newsbf02.news.aol.com Message-ID: <4h8fk9$6nj@newsbf02.news.aol.com> Reply-To: bhade@aol.com (BHade) NNTP-Posting-Host: newsbf02.mail.aol.com Would like to ask some questions to some knowledgable person. I have a different slant on genetic inheritance based on palmar creases . From owner-gene-linkage@net.bio.net Sun Mar 03 22:00:00 1996 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!mr.net!news.mr.net!visi.com!usenet From: "Richard E. McClain" Newsgroups: bionet.molbio.gene-linkage Subject: alzheimer's Date: Mon, 04 Mar 1996 16:14:20 -0600 Organization: Vector Internet Services, Inc. Lines: 6 Message-ID: <313B6B3C.6183@visi.com> NNTP-Posting-Host: ppp23.visi.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0GoldB1 (Win95; I) There's a very good book available on familial Alzheimer's. It's a biography of a woman who lost her mother, two sisters and two brothers to Alzheimer's. It's available at: http://choicemall.com/minnesota/mn001-01 R. McClain From owner-gene-linkage@net.bio.net Tue Mar 05 22:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!jussieu.fr!oleane!tank.news.pipex.net!pipex!newsfeed.internetmci.com!gatech!concert!news-server.ncren.net!taco.cc.ncsu.edu!news From: "Christopher J. Basten" Newsgroups: bionet.molbio.gene-linkage Subject: Summer Short Course Date: Tue, 05 Mar 1996 16:40:13 -0500 Organization: North Carolina State University Lines: 36 Message-ID: <313CB4BD.E56@esssjp.stat.ncsu.edu> Reply-To: basten@esssjp.stat.ncsu.edu NNTP-Posting-Host: esmaccb.stat.ncsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; PPC) This is an announcement for the Summer Institute in Statistical Genetics to be held at North Carolina State University June 6-18, 1996. A series of short courses in statistical genetics will be held at North Carolina State University during the two-week period June 6-18, 1996. The courses will be aimed at geneticists wishing to acquire statistical skills as well as statisticians wishing to become acquainted with genetic applications. Prerequisites are minimal, and the modular nature of the Institute will enable participants to select a program to suit their background and interests. Point your WWW Browser to http://www2.ncsu.edu/ncsu/CIL/stat_genetics/ and follow the link to the Summer Institute, or go directly to http://www2.ncsu.edu/ncsu/CIL/stat_genetics/summer.html for more detailed information. To receive a text version of the web page or if you have any other specific questions, contact me via email, phone or fax. Chris ________________________________________________________________________ Christopher J. Basten Phone: (919)515-1934 Department of Statistics Fax: (919)515-7315 North Carolina State University Email: basten@esssjp.stat.ncsu.edu Raleigh, NC 27695-8203 Location: Cox Hall 608C URL: http://www2.ncsu.edu/ncsu/CIL/stat_genetics/basten.html ________________________________________________________________________ From owner-gene-linkage@net.bio.net Wed Mar 06 22:00:00 1996 Path: biosci!MOREL.UOREGON.EDU!freitag From: freitag@MOREL.UOREGON.EDU (Michael Freitag) Newsgroups: bionet.molbio.gene-linkage Subject: Function of non-coding sequences/ secondary structure Date: 6 Mar 1996 16:50:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <507@reservoir.win-uk.net> NNTP-Posting-Host: net.bio.net Hi there, I am interested in estimating the likelihood of particular short sequences of DNA folding into unusual secondary structures such as cruciforms, hairpins etc. The sequences in question are 200 to 400 bp long and some of them code for 5S RNA (therefore they have inherently a propensity to form unimolecular secondary structures in solution). I wonder whether anybody can point me in the direction of software that would allow input of dsDNA sequence and estimation of free energy of folding. I looked in the literature, but most studies pertain to very short sequences in vitro. Thanks so much, Michael Freitag Univ. of Oregon (541)-346-5197 On Mon, 4 Mar 1996, Shane McKee wrote: > recombination hot-spots near repeats etc - all of these turn out > to be importants genomic features, despite the simplicity of their > coding DNA sequences. > You've hit upon one of my favourite notions here - that repeats > (which are often highly polymorphic) may be able to influence > gene expression, and thus act as a further source of evolutionary > variability without affecting protein structure or expressor > sequences (which are more dangerous things). > The twists and coils and higher structure of the DNA molecule and > chromosome are often quite complex, but in a different sense from > what we're talking about here. For instance, slight changes in > sequence are unlikely to bring about much change in this structure > (correct me if I'm wrong, folks). From owner-gene-linkage@net.bio.net Wed Mar 06 22:00:00 1996 Path: biosci!genetics.adelaide.edu.au!rsaint From: rsaint@genetics.adelaide.edu.au Newsgroups: bionet.molbio.gene-linkage Subject: Faculty Position in Genetics Date: 6 Mar 1996 23:16:19 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 50 Sender: daemon@net.bio.net Distribution: world Message-ID: <01I22DGOD5GMB7CCXL@mulga.itd.adelaide.edu.au> NNTP-Posting-Host: net.bio.net TWO LECTURESHIPS IN GENETICS Applications are invited for two Lectureships in genetics in the Department of Genetics, University of Adelaide, Australia. Lecturer (tenurable) (Ref: 8893) Lecturer (limited term, 3 years) (Ref: 8892) The successful applicants, who will have an appropriate doctoral degree (or equivalent qualification) and a record of productive and innovative research, will be expected to establish vibrant research programs and teach in various undergraduate genetics courses. Research areas of particular interest are those that strengthen or extend current areas of expertise within the Department and that will provide high quality training for postgraduate students. These include (but are not limited to) any aspect of human genetics, neurogenetics, behavioural genetics, genome and chromosome structure and function, gene expression and developmental genetics. It is expected that one of the two appointees will be actively involved in human genetics research. The Department of Genetics has excellent postgraduate and research programs with strengths in gene expression, chromosome structure, developmental genetics, cell cycle genetics, evolutionary genetics and genetic engineering of plants and microbes. Affiliates include members of the Department of Cytogenetics and Molecular Genetics, the Women's and Children's Hospital, the Evolutionary Biology Unit of the South Australian Museum and the South Australian Forensic Science Centre. The positions are available from 1 July 1996. Further details about the Department and duties of the positions, including a selection criteria, may be obtained from Professor Robert Saint, Department of Genetics, telephone 61-8-303 4043, facsimile 61-8-303 4399 or via http:// www.science.adelaide.edu.au/genetics/home.html. Salary per annum: Lecturer (Level B): Aust$42,198 - $50,111 Applications, in duplicate, quoting reference numbers 8893/8892 and giving full personal particulars (including whether candidates hold Australian permanent residency status), details of qualifications, current salary and names and full addresses of three referees should reach the Director, Personnel Services, University of Adelaide, Australia 5005, no later than 12 April 1996. Applicants should clearly address the selection criteria in their applications. The University reserves the right to make enquiries of any person regarding any candidate's suitability for appointment, not to make an appointment or to appoint by invitation. The university of adelaide is an equal opportunity employer. From owner-gene-linkage@net.bio.net Thu Mar 07 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!usenet From: line.roed@kjemi.uio.no (Line R|ed) Newsgroups: bionet.molbio.gene-linkage Subject: Primers for PCR? Date: 8 Mar 1996 10:02:19 GMT Organization: Universitet i Oslo Lines: 18 Message-ID: <4hp0jb$l5f@ratatosk.uio.no> NNTP-Posting-Host: pckjemi103.uio.no Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 Hi! We are to do PCR on whole blood from dogs. We have no information on sequences, restriction maps or anything - all we want is to get a PCR product of reasonable length (1000-2000 bp). Is there anyone who could suggest what primers to use? We have considered using random primers of ca. length 12 bp. Are there any other suggestions? Please mail us directly: line.roed@kjemi.uio.no Regards, Irina Arsky and Line Roed From owner-gene-linkage@net.bio.net Fri Mar 08 22:00:00 1996 Path: biosci!CORNELL.EDU!gma2 From: gma2@CORNELL.EDU (Gregory M. Acland) Newsgroups: bionet.molbio.gene-linkage Subject: Linkage error messages Date: 9 Mar 1996 13:25:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Can anyone tell me what error generates from LINKAGE the message: "ERROR: Incompatability detected in this family for locus 2" I get this message from one data set, no matter what I do with it, yet I can see no formatting or logical errors. TIA Gregory M. Acland (607) 256-5684 [phone] Center for Canine Genetics & Reproduction (607) 256-5689 [fax] James A. Baker Institute for Animal Health gma2@cornell.edu College of Veterinary Medicine Cornell University Hungerford Hill Rd, Ithaca, New York 14853 From owner-gene-linkage@net.bio.net Fri Mar 08 22:00:00 1996 Path: biosci!CORNELL.EDU!gma2 From: gma2@CORNELL.EDU (Gregory M. Acland) Newsgroups: bionet.molbio.gene-linkage Subject: Re: Linkage error messages Date: 9 Mar 1996 15:37:05 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Re my own message: >Can anyone tell me what error generates from LINKAGE the message: >"ERROR: Incompatability detected in this family for locus 2" > >I get this message from one data set, no matter what I do with it, yet I >can see no formatting or logical errors. >TIA It's OK I figured it out: 1. I'm an idiot; 2. I had specified the wrong number of alleles for the locus. Gregory M. Acland (607) 256-5684 [phone] Center for Canine Genetics & Reproduction (607) 256-5689 [fax] James A. Baker Institute for Animal Health gma2@cornell.edu College of Veterinary Medicine Cornell University Hungerford Hill Rd, Ithaca, New York 14853 From owner-gene-linkage@net.bio.net Mon Mar 11 22:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!usenet.eel.ufl.edu!psgrain!rainrgnews0!news.aracnet.com!news.aracnet.com!not-for-mail From: pangolin@aracnet.com (Pangolin) Newsgroups: bionet.molbio.gene-linkage Subject: Huntington's Date: 11 Mar 1996 14:12:28 -0800 Organization: aracnet.com -- Portland's loudest electrons (info@aracnet.com) Lines: 7 Message-ID: <4i28gc$e2@shelob.aracnet.com> NNTP-Posting-Host: shelob.aracnet.com X-Newsreader: TIN [version 1.2 PL2] I apologize in advance if this is off-topic. Is this newsgroup the one to follow advances in the diagnosis and treatment of Huntington's Chorea? If not, then can you recommend any? Thanks -- --------------------------------------------------------------------------- From owner-gene-linkage@net.bio.net Mon Mar 11 22:00:00 1996 Path: biosci!CORN.CSO.NIU.EDU!t80bad1 From: t80bad1@CORN.CSO.NIU.EDU (Brad A Didion) Newsgroups: bionet.molbio.gene-linkage Subject: new address Date: 12 Mar 1996 07:47:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net From: Brad A. Didion My new email address is: badidion@aol.com From owner-gene-linkage@net.bio.net Tue Mar 12 22:00:00 1996 Path: biosci!agate!howland.reston.ans.net!swrinde!newsfeed.internetmci.com!in2.uu.net!news.new-york.net!news.columbia.edu!konichiwa.cc.columbia.edu!wl101 From: wl101@konichiwa.cc.columbia.edu (Wentian Li) Newsgroups: bionet.molbio.gene-linkage Subject: Linkage Newsletter 10(1), March 96 Date: 13 Mar 1996 23:02:03 GMT Organization: Columbia University Lines: 182 Message-ID: <4i7k5b$i33@apakabar.cc.columbia.edu> NNTP-Posting-Host: konichiwa.cc.columbia.edu Linkage Newsletter Vol. 10 No. 1 March 1996 Published by Postal address: Jurg Ott, Columbia University, New York Columbia University, Unit 58 Email: ott@rockvax.rockefeller.edu 722 West 168 Street WWW: http://linkage.cpmc.columbia.edu New York, NY 10032 Editorial Assistant: Katherine Montague Email: km165@columbia.edu Fax: 212-568-2750 Tel: 212-960-2507 (this and all previous newsletters are available on our ftp site/Web page) EDITORIAL After ten years with Columbia University, the "genetic linkage" group will be moving to Rockefeller University, New York, where a new Laboratory of Statistical Genetics is being formed. The move will take place throughout this summer and will be completed in November of this year. A new ftp site and Web page will be set up at Rockefeller but addresses are not known yet (note Dr. Ott's new email address above). They will be posted on our current ftp site/Web page, which will continue to exist for some time (at least one year). LINKAGE COURSES The next courses in genetic linkage analysis have been scheduled as follows, and interested researchers are urged to apply early as our courses tend to fill up quickly: 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). The second course will be held only with a sufficient number of applications (which we expect). Deadline for applications has been extended to April 8. October 7-11, 1996, at University of Zurich, Switzerland (ad- vanced course, maximum of 12 participants). Deadline for applications is August 30, 1996. October 14-18, 1996, at Rockefeller University (advanced course, maximum of 20 participants, with preference to participants at U.S. inst- itutions and companies). Deadline for applications is August 30, 1996. 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 supple- mental 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 >> Fortran and Windows 95 << The only Fortran program currently distributed by us is LIPED. If compiled with Microsoft (MS) Fortran version 5.10, various compiler switches allow it to run under DOS, OS/2 and Windows 3.1. Under Windows 95, programs compiled for DOS still run in a DOS window; however, programs compiled for Windows 3.1 will not run in Windows 95. Presumably, for Windows 95 an updated Fortran compiler must be ob- tained from Microsoft. If anyone has experience in this matter, suggestions would be appreciated. >> OS/2 and Windows 95 << Even though I was an early fan of OS/2 ever since its version 1.1 came out, "market forces" made me decide that we no longer want to support OS/2 versions of our programs; these versions are still available on our ftp site but they will not be updated. Users with a need for running large programs may find it convenient to turn to our programs compiled with NDP Pascal for DOS. This compiler does not impose any limitations on array sizes, code or data segments, etc. >> FASTLINK 3.0P << (submitted by A. Schaffer) I am pleased to announce that FASTLINK 3.0P is now available. FAST- LINK is a faster version of the main programs in LINKAGE. As of version 2.3P, FASTLINK runs in parallel on either UNIX multiprocessors or networks of UNIX workstations. As with previous versions, the code is available by ftp from: softlib.cs.rice.edu Login as anonymous, leave full e-mail address as password. cd pub/fastlink If you are a UNIX user: get fastlink.tar.Z If you are a DOS user: cd dos If you are a VMS user: get README get README.VMS and follow the instructions there for what you need Retrievers in Europe may find it more convenient to retrieve from the mirror site at: ftp.ebi.ac.uk The instructions are similar, but instead of: cd pub/fastlink (for softlib) do cd pub/software/linkage_and_mapping/FASTLINK/fastlink (for ebi) Among the improvements in FASTLINK 3.0P (compared to 2.3P) are: -- The code runs faster on data sets that have loops or unused alleles. If you used FASTLINK 2.3P, you may have noticed that it printed diagnostics when a data set had unused alleles, but it did not take advantage of the situation. -- UNKNOWN now detects violations of Mendelian rules of inheritance in looped pedigrees. It never did this before. -- maxhap and maxfem are no longer in the code as constants. If you were resetting maxhap each time and recompiling, you won't have to do that any more. If you were setting maxhap unnecessarily high to avoid recompiling, you may perceive some speedup. See the file README.updates for more details on recent code changes in FASTLINK. Some algorithmic aspects of the most recent improvements can be found in: A. A. Schaffer, Faster Linkage Analysis Computations for Pedi- grees with Loops or Unused Alleles, Human Heredity, to appear. This paper can be found as paper5.ps at the ftp sites. Alejandro Schaffer schaffer@nchgr.nih.gov >> Two problems in LINKAGE programs << (submitted by A. Schaffer) Two LINKAGE problems have arisen recently in FASTLINK bug reports that users should be aware of. I call them "problems" and not "bugs" because one has to abuse LINKAGE to get them to happen. Problem 1. If a loop involves someone who is multiply married, and it is unbroken, then LINKAGE might not go into an infinite loop. If it doesn't, plausible but wrong results are printed. I have now seen 3 pedigrees with this problem. This is not a bug because if one uses MAKEPED with LOOPS embedded as one should, the loop will be caught there. Problem 2. If an allele frequency is specified as 0.0 various prob- lems can arise. The one I saw is: -- user specified frequency of first allele is 0 -- data set had a pedigree in which nobody was typed at that locus -- unknown converted everyone to homozygous 1 1 at that locus -- because the allele frequency was 0.0, the likelihood also came back as 0.0, making the log likelihood -infinity. Both problems are also present in all versions of FASTLINK until the most recent (3.0P). I fixed problem 1 with a new diagnostic in UNKNOWN in the initial 3.0P release. I addressed problem 2 with a new warning in the main programs. Support through grant HG00008 from the National Center for Human Genome Research is gratefully acknowledged. From owner-gene-linkage@net.bio.net Wed Mar 13 22:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!in2.uu.net!mozz.unh.edu!usenet From: Thomas.D.Kocher@unh.edu (Thomas D. Kocher) Newsgroups: bionet.molbio.gene-linkage Subject: Software for haploid mapping Date: 14 Mar 1996 20:21:19 GMT Organization: University of New Hampshire Lines: 13 Sender: -Not-Authenticated-[8170] Message-ID: <4i9v3v$3rb@mozz.unh.edu> NNTP-Posting-Host: cichlid.unh.edu X-Posted-From: InterNews 1.0.1b7@cichlid.unh.edu Xdisclaimer: No attempt was made to authenticate the sender's name. We are generating haploid progeny from fish eggs using irradiated sperm to activate development. The process is analogous to sperm-typing of humans, except that we have much more DNA to work with. Now that we are generating tables of haploid genotypes, we need some software to scan for linkages. Can anyone point me to some existing software which could do the trick? Thomas D. Kocher Assoc. Prof. Dept. of Zoology University of New Hampshire Durham, NH 03824 From owner-gene-linkage@net.bio.net Wed Mar 13 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Ivo Wiesner Newsgroups: bionet.molbio.gene-linkage Subject: [Q]:MAPMAKER for PC versus JOINMAP-ivo w. Date: 14 Mar 1996 16:15:56 -0000 Lines: 9 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4i9gns$f6d@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: gen-link@dl.ac.uk Dear Netters, which are your experiences with Mapmaker for PC versus Joinmap software for calculation of F2 intercross genetic maps (incl. graph.output quality)? Is it worth to buy expensive Joinmap? ThanX in advance for any comments. Ivo Wiesner From owner-gene-linkage@net.bio.net Thu Mar 14 22:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!in2.uu.net!newsflash.concordia.ca!news.nstn.ca!news.cs.indiana.edu!umn.edu!newsstand.tc.umn.edu!lenti From: dean@lenti.med.umn.edu (Dean Flanders) Newsgroups: bionet.molbio.gene-linkage Subject: BIONET.MOLBIO.GENE-LINKAGE.FAQ Date: 15 Mar 1996 06:00:23 GMT Organization: University of MN, Medical School Lines: 984 Message-ID: <4ib11n$61r@epx.cis.umn.edu> NNTP-Posting-Host: lenti.med.umn.edu Originator: dean@lenti.med.umn.edu BIONET.MOLBIO.GENE-LINKAGE FREQUENTLY ASKED QUESTIONS (FAQ) AS OF 1996/22/96 1.0) FAQ ADMINISTRATIVE INFORMATION [1995/05/18] 1.1) Where can I obtain and/or access the bionet.molbio.gene-linkage FAQ? [1995/03/01] 1.2) Who created the bionet.molbio.gene-linkage FAQ? [1995/03/01] 1.3) How can I help improve this FAQ? [1995/03/01] 1.4) Contributors to this FAQ. [1995/09/09] 1.5) When was the FAQ last updated? [1996/22/96] 2.0) INFORMATION RESOURCES 2.1) What anonymous FTP sites have programs/utilities useful for linkage analysis? [1995/03/01] 2.2) What books are helpful when learning about linkage analysis? [1995/03/01] 2.3) What WWW sites have useful linkage information? [1996/01/02] 2.4) What gopher sites have useful linkage information? [1995/03/01] 2.5) What "linkage centers" make information and assistance available to researchers? [1995/12/11] 2.6) What journals are useful for linkage analysis? [1995/06/02] 2.7) What courses are offered in linkage analysis? [1995/09/09] 3.0) GENE-LINKAGE SOFTWARE OVERVIEW 3.1) What database management programs do people use for linkage data? [1995/05/31] 3.2) What programs are available for pedigree drawing? [1995/04/01] 3.3) What linkage analysis helper programs are available? [1995/04/01] 3.4) Why are some programs used primarily for chromosome mapping, while others are used for disease mapping? [1995/03/01] 3.5) What programs are used for physical mapping? [1995/11/30] 3.6) What programs are used for disease gene mapping? [1995/09/07] 3.7) What programs are available for running genetic simulations? [1995/11/30] 3.8) What programs are available to help detect errors in linkage data? [1995/11/30] 3.9) What programs help me recode genetic markers? [1995/03/01] 4.0) LINKAGE PACKAGE SPECIFIC INFORMATION 4.1) How do I get my CEPH data into CRI-MAP format? [1995/03/01] 4.2) How do you calculate MAXHAP? [1995/09/09] 4.3) When should you use binary coding instead of numeric allele coding? [1995/03/01] 4.4) What do you do when allele frequencies do not add up to 1; for example, when alleles are not present in a pedigree under study? [1995/03/01] 4.5) I use LINKAGE and/or FASTLINK. Which references should I include in my papers? [1995/03/01] 4.6) What is recoding of alleles all about anyway? [1995/03/01] 4.7) What do you do when you get thetas greater than 0.5 when using linkage? [1996/22/96] 5.0) COMPUTER ADMINISTRATION AND OPTIMIZATION 5.1) How w can I increase the speed of the LINKAGE/FASTLINK package on my workstation? [1995/05/18] 6.0) MOLECULAR BIOLOGY ISSUES IN LINKAGE ANALYSIS 6.1) What screening sets are available for linkage analysis? [1995/09/14] 1.0) FAQ ADMINISTRATIVE INFORMATION 1.1) Where can I obtain the bionet.gene-linkage FAQ? [1995/03/01] It is available by anonymous FTP from lenti.med.umn.edu in /pub/linkage. The best way to view the FAQ is via the WWW, from http://lenti.med.umn.edu/linkage/linkage.html. The FAQ is also available via gopher at lenti.med.umn.edu in /Biologically Related Information/Linkage Analysis. The FAQ will also be posted in the USENET groups bionet.molbio.gene-linkage and news.answers the 1st and 15th of each month. 1.2) Who created the bionet.molbio.gene-linkage FAQ? [1995/03/01] Darrell Root (rootd@ohsu.edu) originally started the bionet.molbio.gene-linkage FAQ in May of 1994 in an attempt to share information and experiences that may be of use to other people involved in linkage analysis. I am Dean Flanders (dean@lenti.med.umn.edu), the current maintainer of the FAQ, and began my tenure in December of 1994. The FAQ will never serve as a short course in linkage analysis, but instead it will ideally be a place to help beginners get started in the area and to help experts not make the same mistakes as others. All of the information in this FAQ by no means comes completely from Darrell or me, but from a large number of people that work in the area of linkage analysis. Their names are listed at the end of this section of the FAQ. 1.3) How can I help improve this FAQ? [1995/03/01] Feel free to send any information that you think would be beneficial for other people who are just beginning in linkage or have been doing linkage for years to linkage@lenti.med.umn.edu. Also, if there is information you would like to see or errors in this FAQ please let us know by sending email to linkage@lenti.med.umn.edu. If you would like to see something changed or added to the FAQ please to send it in a format that can be quickly incorporated into the FAQ, such as correcting the errors in the section of the FAQ and emailing it back to the FAQ maintainer. 1.4) Contributors to this FAQ. [1995/09/09] David Adler, John Attwood, Michael Boehnke, Marcia Brott, Don Bowden, Michael Braverman, Lucien Bachner, Young B Choi, Kevin Crawford, Dave Curtis, Peter Doris, Bennett Dyke, David Featherstone, Dean Flanders, Jonathan Haines, Rob Harper, Pierre Janssens, David Kikuchi, Wentian Li, Tim Little, Tara Matise, Eli Meir, Mike Miller, Jurg Ott, Darrell Root, Alex Schaffer, Robert Stodola, Frank Visser, Dan Weeks, Ellen Wijsman, Scott Wildenberg, Matthias Wjst, and Kim Worley. 1.5) When was the FAQ last updated? [1996/22/96] The last update of the FAQ was on 1996/22/96. All sections should indicate what month and year they were last updated. In addition one can go to the list of updates that are maintained at http://lenti.med.umn.edu/linkage/gefaqup.html. This is a list in chronological order of updates with direct links to the updates in the FAQ. 2.0) INFORMATION RESOURCES 2.1) What anonymous-FTP sites have programs/utilities useful for linkage analysis? [1995/03/01] At present there is no one site that serves as a repository for all linkage software. So the best way of finding FTP site information is to read the software package information below, which should provide all of the necessary FTP information. 2.2) What books are helpful when learning about linkage analysis? [1995/03/01] Bishop, M. J. "Guide to Human Genome Computing." Academic Press, 1994. Davies, K. E. "Human Genetic Diseases - A Practical Approach." IRL Press, Oxford England and Washington, D.C., 1986. Dracopoli, N. C., Haines, J. L., Korf, B. R., Moir, D.T., Morton, C. C., Seidman, C. E., Seidman, J. G., Smith, D. R. "Current Protocols in Human Genetics." John Wiley and Sons, Inc., USA, 1994. Khoury, M. J., Beaty, T. H., and Cohen, B. H. "Fundamentals of Genetic Epidemiology." Oxford University Press, 1993. Ott, J. "Analysis of Human Genetic Linkage." Johns Hopkins University Press, 1991. Terwilliger, J. D. and Ott, J. "Handbook of Human Genetic Linkage," Johns Hopkins University Press, 1994. Thompson, E. A. "Pedigree Analysis in Human Genetics." Johns Hopkins University Press, Baltimore and London, 1986. 2.3) What WWW sites have useful linkage information? [1996/01/02] This is in no way an attempt to list the explosion of WWW sites of biological interest on the Internet, but it is a listing of some of the major ones and ones of particular interest in linkage analysis. http://www.yahoo.com/Science/Biology/Genetics/, this is a list of sites related to genetics that is kept very up to date. http://www.gdb.org/Dan/DOE/intro.html, this is a short course of sorts that gives some very basic information on how to go about gene mapping. http://lenti.med.umn.edu/linkage/linkage.html, which is serving as linkage analysis home page, will have links to all of the WWW sites listed as well as gopher servers and a hypertext version of the FAQ. http://www.genethon.fr, the Genethon Center, Genethon's home page. http://www.chlc.org, the Cooperative Human Linkage Center, CHLC's home page. http://gdbwww.gdb.org has a version of GDB available and access to OMIM. http://www.pathology.washington.edu has human and mouse standard idiograms. The idiograms are useful for making illustrations for gene mapping and for constructing abnormal chromosomes. The PostScript idiograms can be manipulated band by band with illustration software such as Adobe Illustrator, Aldus FreeHand, Canvas, and Altsys Virtuoso. http://www.gene.ucl.ac.uk/~john/programs.html contains software by John Attwood. http://www.gene.ucl.ac.uk/packages/dcurtis/ contains software by Dave Curtis. http://linkage.cpmc.columbia.edu has a lot of useful information on linkage analysis; in particular it offers information on software, the course offered by J. Ott, and the Linkage Newsletter. 2.4) What gopher sites have useful linkage information? [1995/03/01] There is one that will be maintained with links to other gophers of interest in linkage analysis, as well as links to other gopher servers of biologically related information. It is at lenti.med.umn.edu, and the path to it is Biologically Related Information/Genetic Linkage Analysis. 2.5) What "linkage centers" make information and assistance available to researchers? [1995/11/11] One such center is the Cooperative Human Linkage Center (CHLC). The goal of this center is to generate a high resolution map of the human genome and rapidly distribute this information to the genome community. They are in the process of identifying more human markers and developing high resolution framework maps. One can obtain information about CHLC from via gopher from gopher.chlc.org , http://www.chlc.org , ftp://ftp.chlc.org , info-server@chlc.org, or help@chclc.org. Among other things, CHLC provides primer selection and linkage analysis via email. Information on those services can be found by sending email to: primer- server@chlc.org and linkage-server@chlc.org. David Featherston (davidf@caos.kun.nl) from the Dutch EMBnet Node is starting a linkage analysis service: software availability, support/advice initially, possibly training, and perhaps consultancy. At present they have MapMaker/EXP 3.0b, MapMaker/QTL 1.1, Lathrop and Lalouel's LINKAGE package, and Schaffer's FASTLINK package. This means that if users have Genomics Package accounts at the CAOS/CAMM Center, they can use these programs on their fast computers to analyze their data sets. Please contact David Featherston if you are interested in more information about such an account. A major European center is the Human Genome Mapping Project Resource Centre in Hinxton, England. It is funded by the Medical Research Council, and has a broad range of software and databases available, mainly focused on the Human Genome Project. In the area of Linkage analysis it has the following programs available: FASTLINK, CRIMAP, MAP MAPMAKER, HOMOZ, PEDPACK, APM, SIMLINK, FASTMAP, COMDS, DOLINK & QDB, HANDLINK, GAS and Jurg Ott's collection of programs. The aim is to have all major (Unix-based) gene linkage packages available for our users. The Center also gives courses on linkage analysis. More information about the Centre can be obtained from it's home- page: http://www.hgmp.mrc.ac.uk/. If you want to register as user, send e-mail to admin@hgmp.mrc.ac.uk for a registration form. For more information about the gene-linkage services you can contact Frank Visser (fvisser@hgmp.mrc.ac.uk). INFOBIOGEN: This is the French GDB node that offers also a linkage server and assistance in the process of linkage analysis. It uses LINKAGE, FASTLINK and other programs running on a Sparc Center 2000E with 1 giga RAM, 4 Gig of swap, and 6 CPU's. For furhter information contact Lucien Bachner at bachner@infobiogen.fr or look at the following web site http://www.infobiogen.fr/. 2.6) What journals are useful for linkage analysis? [1995/06/02] American Journal of Human Genetics, Annals of Human Genetics, Computer Applications in Biosciences (CABIOS), Genomics, Genetic Epidemiology, Human Genome News (available by gopher from gopher.gdb.org), Human Genome Project Journal, Human Heredity, Journal of Computational Biology, Nature Genetics. 2.7) What courses are offered on linkage analysis? [1995/09/09] There are three primary courses offered throughout the yeart on human linkage analysis. One is a four day course offered once per year by Drs. Margaret Pericak-Vance and Jonathan Haines. The next course will be offered in late April, 1996 in Boston. The focus of the course is on the overall design of a human disease gene mapping study, with particular emphasis on the problems of common/complex disorders. The course covers clinical classification, pedigree ascertainment, collection, and follow-up, basic linkage techniques, linkaghe and association analysis for complex disorders, laboratroy technqiues for genotyping, and gene characterization. The courseemphasizes the global decision-making process, rather than details of specific techniques. For more information write to Genetic Methods Course; c/o Dr. Margaret Pericak- Vance; Division of Neurology, Box 2900; Duke University Medical Center; Durham, NC 27710, or you can send e-mail to genclass@genemap.mc.duke.edu. The remaining two courses are both offered by Jurg Ott on the software used for human linkage. One is a beginner's course, and the other an advanced course for those familiar with the linkage analysis software. These courses are offered several times throughout the year and you can get more information by contacting Katherine Montague/Jurg Ott; Columbia University, Unit 58; 722 West 168th Street; New York, NY 10032. In addition you can fax to (212)568- 2750 or call (212)960 2507 or email km165@columbia.edu for more information. A new beginner's level linkage course will be offered in French October 24-25 1995 by INFOBIOGEN, in Villejuif south suburb of Paris. It's free for all academic institutions. For furhter information contact Lucien Bachner at bachner@infobiogen.fr or linkage@infobiogen.fr. 3.0) GENE-LINKAGE SOFTWARE OVERVIEW 3.1) What database management programs do people use for linkage data? [1995/05/31] One must be aware that some pedigree drawing software can also serve as databases for data as well as drawing pedigrees, see the next question in the FAQ for a description of those packages. CEPH DBMS: The CEPH DataBase Management System is specifically designed for chromosome mapping with CEPH style pedigrees. It can output data in ped.out format for the LINKAGE package. This program can now be picked up via anonymous FTP from ftp.cephb.fr in pub/ceph_genotype_db. DOLINK: This DOS custom database program by D. Curtis manages genetic data and sets up input files for linkage analysis. It is available from ftp.gene.ucl.ac.uk. The DOS and Windows versions of DOLINK program help manage genetic data and setup analysis. It is available with the C++ source allowing compilation on Unix host running X and possibly a Macintosh. File Express: This is a DOS shareware database which can be used to hold data for DOLINK (largely superseded by QDB). It is available as fe51-a/b/c.zip via FTP from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. LABMAN and LINKMAN: These are linkage analysis databases for holding linkage data and exporting it in various formats for linkage analysis. They are available via anonymous FTP from lenti.med.umn.edu in /pub/linkage/labman. These databases were developed by P. Adams of Columbia University. LYNKSYS: This custom-made database program was written by J. Attwood and S. Bryant. Although they continue to use it, J. Attwood suggests using DOLINK instead. LINKSYS is not currently available at any FTP sites. Map Manager: It is a program for the Macintosh which helps analyze the results of genetic mapping experiments using backcrosses, intercrosses, or recombinant inbred strains. In addition it also has tools for statistical analysis of experiments. The program was created by K. F. Manly at the Roswell Cancer Institute and is available via FTP from mcbio.med.buffalo.edu in /pub/MapMgr. QDB: This is a database program available as DOS and Windows versions and with C++ source allowing compilation for X and possibly Macintosh. It is available as qdb16a.zip via FTP from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. 3.2) What programs are available for pedigree drawing? [1995/04/01] One of the tricks of managing individuals in a mapping study is trying to get the database you are using to export your family data in a format acceptable for input into pedigree drawing programs. The marriage between these two can be of great assistance. However, some pedigree drawing programs have databases as a part of the package. CYRILLIC: This is a pedigree editor for Windows with facilities for including marker data which you can then have it output the input files for LINKAGE. It is Windows-based, so input of the pedigree is very efficient. You also have a data form associated with each individual where you can store names and other pertinent data. It also has the ability to interface with most standard PC databases. This program is not public domain and is available from Cherwell Scientific Publishing. If you would like more information send email to csp@sable.ox.ac.uk and they would be very happy to send you a demo of the program. Version 2 of Cyrillic should be coming out late summer of 1995. FTREE: This is a DOS pedigree program written by R. Go at the University of Alabama. GENETREE: GeneTree 1.0 is a DOS package which provides a convenient way to draw family tree diagrams suitable for genetics or genealogy. The package consists of the GeneTree program, which draws pedigree diagrams using a command language; and SC, using a menu driven program that facilitates creation of GeneTree commands. GeneTree and SC are made available with program manuals, examples of family tree diagrams, and a GeneTree Quick Reference Guide. GeneTree is written in C. Note that it is a DRAWING program and does not compute genetic parameters. The GeneTree program is available from wijsman@max.u.washington.edu at a price of $125 (because of licensing fees from a private company which wrote one of the drivers used in the program). KINDRED: This new DOS database program, distributed by Epicenter Software, is specifically designed for linkage analysis. A free demo is available by calling (818)-304-9487. In addition to database duties, this program will draw pedigrees, haplotype marker data, and can output data in LINKAGE format. PEDPAK: This package is designed to handle large datasets for animals. The package was written and distributed by Alan Thomas, who is in Bath, England. The software is not public domain and must be purchased. Pedigree/Draw: It is a Macintosh based program, written by B. Dyke, P. Mamelka, and J. MacCluer. It is available from bdyke@darwin.sfbr.org or Pedigree/Draw; Department of Genetics; Southwest Foundation for Biomedical Research; PO. Box 28147; San Antonio, TX 78228-0147. An upgrade from a previous version is $10, the current version is 4.4. Documentation costs $10 printed and the full package including documentation costs $45. There is a script which converts linkage format to Pedigree/Draw available via anonymous FTP at ftp.ee.pdx.edu in /pub/users/cat/rootd/convert.new. PEDRAW: This program is a pedigree drawing program written by D. Curtis for DOS and available via FTP from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. The most current version is called pedraw16.zip. A companion program to PEDRAW is PEDHELP, it is a pop-up help for PEDRAW. PAP: The Pedigree Analysis Package (PAP) is a set of FORTRAN 77 programs for computing likelihoods and simulating phenotypes of genetic models on pedigrees. It is available via gopher from corona.med.utah.edu in Publicly Accessible Software, probes(sts), etc./software/pap. 3.3) What linkage analysis helper programs are available? [1995/04/01] CEPH2CRI: This program converts to output from the CEPH DBMS into the format useable in CRI- MAP. It can be found at ftp.gene.ucl.ac.uk in /pub/packages/linkage_utils. EASISTAT: This is a DOS statistics package, it contains EASIGRAF which draws graphs of lod scores from the output of FASTMAP. The lod scores first need to be run through the TABLE utility, which is included in the DOLINK and FASTMAP packages. It is available as estat21.zip via anonymous FTP from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. FIRSTORD: A demonstration of a method for preliminary ordering of loci based on two-point lod scores. It is available as DOS executable and C source called first11.zip from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. LINKMED: A program for converting LINKAGE-format files to MENDEL-format files. It is available by anonymous FTP from watson.hgen.pitt.edu as linkmend.tar.Z. MAP: A program to convert LINKMAP output into a table of multipoint lod scores. It is available by anonymous FTP from watson.hgen.pitt.edu as map.tar.Z. PEDREP: A program for converting a MENDEL-format pedigree file ('pedm.dat') to a Pedigree/Draw file for graphical display on a Macintosh. It is available by anonymous FTP from watson.hgen.pitt.edu as pedprep.tar.Z. RECODE: A program for recoding character or sized-allele data into numbered-allele data. It is available by anonymous FTP from watson.hgen.pitt.edu as recode.tar.Z. 3.4) Why are some programs used primarily for human chromosome mapping, while others are used for human disease mapping? [1995/03/01] Any family can be used for chromosome mapping, so CEPH has picked a particular family "shape" and generated a large database with these families. Programs designed for chromosome mapping can be optimized for using these families, reducing the time needed for calculations. Only families afflicted with a disease can be used for disease gene mapping. As a result, programs designed for disease gene mapping need to be able to deal with arbitrary pedigrees. In addition, these programs need to be able to handle incomplete penetrance. 3.5) What programs are used for physical mapping? [1995/11/30] CLINKAGE: This is the special version of the LINKAGE programs for 3-generation CEPH pedigrees and codominant markers. The PC and VAX versions are available by FTP from linkage.cpmc.columbia.edu. The Unix version is available from corona.med.utah.edu. CHROMLOOK: This is a program for generating haplotypes of marker data in nuclear pedigrees with all individuals genotyped. It identified both the maternal and paternal recombination events, and provides the resulting haplotypes and recombinants in an easy-to-read format. It should be available via FTP server sometime this summer. It was written by Jonathan Haines and he can be contacted at haines@helix.mgh.harvard.edu. CINTMAX: This program is an extensively modified version of CILINK. It uses map functions to model the transmission of gametes from parent to child. Some of these map functions are multilocus feasible, and so can be used with more than 3 loci at a time. It is available by anonymous FTP from watson.hgen.pitt.edu as cintmax.tar.Z. CRI-MAP: This program has been used for chromosome mapping for years. It has options which can generate maps, calculate order probabilities, and printout recombination data. It works on .gen files with data from CEPH style families. It is written in K& R type C code, and the author Phil Green has successfully ran it on Unix, DOS, VMS, and Macintosh systems. It is not available via anonymous FTP. Phil Green distributes CRI-MAP freely ONLY to academics/academic institutions. Contact him at: Phil Green; Molecular Biotechnology Dept., FJ-20; Fluke Hall on Mason Rd.; Univ. of Washington; Seattle, WA 98195; USA; Phone (206) 685-4341; Fax (206) 685-7344; or email phg@u.washington.edu. FASTMAP: This program produces quick approximation to multipoint lod score, available as a DOS executable and C source as fstmap11.zip from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. MULTIMAP: This LISP based expert system uses an customized version of CRI-MAP to create a chromosome map. It is available via anonymous FTP from chimera.gene.cwru.edu. The authors T. Matise, M. Perlin, and A. Chakravarti continue to improve the code, add new functions, and provide excellent support. When used with the CRI-MAP chrompic option (to find double-recombinations to identify possible errors), it is incredibly useful. This is Unix-only (supported for DEC-Ultrix, HP9000, and Suns). The customized CRI-MAP version (called LISPCRI) is distributed at the FTP site, but was not meant to be used independently of MULTIMAP. MAPMAKER: Dr. Eric Lander; Whitehead Institute; 9 Cambridge Center; Cambridge, MA 02142; mapm%mitwibr@mitvma.mit.edu. MAPMAKER is available via FTP at genome.wi.mit.edu in /pub/mapmaker3. RHMAP: It is a set of three FORTRAN 77 programs that provide the means for a complete statistical analysis of RH mapping data. RH2PT is a program for data description and two-point analysis. It provides estimates of locus-specific retention probabilities and pairwise breakage probabilities, two-point lod scores for linkage of the various marker pairs, and linkage groups. RHMAP is now also available at the following URL http://www.sph.umich.edu/group/statgen/software. If you would like email notification of updates please send email to boehnke@umich.edu. 3.6) What programs are used for disease gene mapping? [1995/09/07] APM: The Affected Pedigree Member Method distribution contains the new APM programs, a new file conversion utility, and a histogram/statistics generator. To build the entire distribution, you need C, Pascal, and FORTRAN compilers, and a make utility is also helpful. The programs which are built include: APM, a program to calculate the single locus statistic over one or several marker loci; SIM, a program to simulate pedigrees and, using output files of APM, test for asymptotic normality of the null distribution; APMMULT, a program to generate the multilocus statistic; SIMMULT, a program like SIM but which simulates recombination and uses the output of APMMULT; CHAPM, a program to convert LINKAGE files to APM files, or APM files of one format to APM files of another format; and HIST, a program to compute various statistical figures, plot a histogram, and compute empirical p-values. The APMember package by D. Weeks is available via anonymous FTP from watson.hgen.pitt.edu. Additionally, there are pre-compiled executables of the APM programs for Sun-OS and Sun-Solaris available as newapm.sunos.tar.Z newapm.solaris.tar.Z. CLUMP: A Monte Carlo method for assessing significance of a case-control association study with a multi-allelic marker, available as DOS executable and C source. It is available as clump.zip via anonymous FTP from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. ESPA: This is a program used for extended sib pair analysis. It comes in a DOS version and can only look at markers containing 5 alleles. It was written by Lodeijk Sandkuijl and can be obtained by writing to him at Voorstraat 27; Delft 2611 JK; THE NETHERLANDS. ERPA: A program for carrying out nonparametric linkage analysis, available as DOS executable and C source. It is called erpa12.zip via anonymous FTP at ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. FASTLINK: This is a much faster implementation of the main programs in LINKAGE (LODSCORE, ILINK, MLINK, LINKMAP) in C. The code is faster due to the use of new and better algorithms for the time intensive parts of the computation. FASTLINK is distributed by A. A. Schaffer from the FTP site softlib.cs.rice.edu (cd pub/fastlink). Version 1 of FASTLINK was instigated by R. W. Cottingham Jr. with implementation done by R. M. Idury and A. A. Schaffer. Version 2 of FASTLINK includes further improvements implemented by A. A. Schaffer, S. K. Gupta, and K. Shriram, with guidance from R. W. Cottingham Jr. Version 2 includes the capability to recover gracefully from a crash of the computer on which FASTLINK is running. FASTLINK was initially intended for UNIX machines, but the distribution now includes instructions for porting to VMS as well as a version for DOS. FASTLINK allows you to compile in "fast" or "slow" mode (the slow version of FASTLINK is still much faster than the old LINKAGE programs). The "fast" version uses lots of memory, but uses the extra memory to contain some of the intermediate results which are repetitively recalculated in the "slow" version (and the old linkage package). Best speed can be obtained by setting up 300 megs of virtual memory on a Unix workstation and using the "fast" version. Schaffer maintains a mailing list of fastlink users (fastlink-list@cs.rice.edu) to answer queries and keep users up to date. Schaffer, Gupta, and other colleagues at Rice University have implemented parallel versions of FASTLINK for either a shared-memory multiprocessor or a network of UNIX workstations. This version is now available as FASTLINK 2.3P at the above mentioned FTP site. Write to schaffer@cs.rice.edu for more information. GAS: It provides facilities for reading, writing, sectioning and performing statistical analyses on phenotypic and genotypic data and one of its features is sib pair analysis. It has been developed within the Department of Medicine at Oxford University and is available via FTP from well.ox.ac.uk in the directory pub/genetics/gas. GREGOR: It is a piece of DOS based software for producing simulated genetic data. It does not perform linkage analysis, but it may be useful for testing methods or assumptions about linkage analysis. GREGOR is operated by a series of hierarchical menus that permit the user to define hypothetical genetic scenarios (gene positions and effects) and produce simulated data-sets for a variety of population structures. GREGOR is available by FTP from the site sifon.cc.mcgill.ca in pub/McGill-Contrib. Questions should be directed to the authors tinker@agradm.lan.mcgill.ca or mather@agradm.lan.mcgill.ca. LINKAGE: This package of programs was developed by M. Lathrop with help from J. M. Lalouel, C. Jlier, and J. Ott. The LINKAGE package consists of several analysis and several utility programs. Versions are available for DOS, OS2, VAX, and Unix platforms. Here are some of the analysis programs: MLINK: 2-point lod-score calculations at fixed recombination distances; LINKMAP: multipoint lod score calculations at fixed distances; ILINK: calculates the recombination distance with the highest lod-score. Unix versions are available via gopher from corona.med.utah.edu in Publicly Accessible Software, probes(sts), etc./software/linkage, DOS and VMS versions are available from linkage.cpmc.columbia.edu, or on floppy disks, when you write to: Katherine Montague/Jurg Ott; Columbia University, Unit 58; 722 West 168th Street; New York, NY 10032. Send pre-formatted DOS disks if you request linkage by mail. You can send email to km165@columbia.edu if you need more information regarding mail requests for the LINKAGE package. LIPED: This DOS program written by J. Ott calculates probabilities for linkage between disease markers and genetic markers. Its input file differentiates between phenotypes and genotypes. As a result, this program is easiest to use when your data is from "old-style" genetic-markers (such as blood phenotype data). This was one of the first programs to do linkage analysis calculations, the LINKAGE package is more commonly used now. SAGE: Statistical Analysis Package for Genetic Epidemiology is composed of 18 programs: AGEON: Estimating the Distribution of Age-of-Onset, ASSOC: marker-trait Associations in Pedigree Data, BCROSS: Genetic Hypothesis for Quantitative Data on Inbred strains, their F1 and Backcross(es), CLUSTR: Power Transformation to Obtain Normality and Homoscedasticity from Clustered Data, FCOR: Family Correlations, FSP: Family Structure Program, LODLINK: Lod Score Linkage Analysis, MAPLOC: Mapping a Disease Related Trait Relative to a Set of Linked markers, MAXFUN: Function maximization Subroutine, REGC,REGD,REGTL,REGTN: Segregation Analysis Programs, RELATE: Relationship to Proband, SIBPAL: Sib-Pair Linkage Analysis, and DBSORT, RENUM, SPLIT: Toolkit Programs. Author Dr. R.C. Elston, address Department of Biometry and Genetics; Louisiana State University Medical Center; 1901 Perdido Street; New Orleans, Louisiana 70112, USA. The email contact address is sage@haldne.biogen.lsumc.edu. It is available for the following operating systems: VAX, SunOS 4.1.x, Apple Macintosh II, and DOS. This program is not shareware and must be bought. X-LINKED APM: X-linked version of the APM programs (single-marker), see APM above for more information on APM. It is available by anonymous FTP from watson.hgen.pitt.edu as xlinkapm.tar.Z. Also, xlinkapm.readm is available there, which is a readme about the X-linked version of the APM programs. 3.7) What programs are available for running linkage simulations? [1995/11/30] FASTSLINK: This is program is just like SLINK (see SLINK below), but it utilizes the enhancements incorporated into FASTLINK. It is available via anonymous FTP from watson.hgen.pitt.edu. SIMAPM: Is the SLINK based simulation program for the APM package. This represents a hacked together package which only runs under a Unix system. You will need FORTRAN, Pascal, and C compilers to use this package. It is available via anonymous FTP from watson.hgen.pitt.edu SIMLINK: This FORTRAN program developed by L. Ploughman and M. Boehnke simulates linkage analysis on a family, and gives you an estimate the probability, or power, of detecting linkage in a given family. It allows the researcher to determine whether a family has sufficient informativeness to detect linkage. SIMLINK requires large quantities of memory. It was written for DOS, but has been ported to many platforms. It is available from: Michael Boehnke; Department of Biostatistics; School of Public Health; University of Michigan; Ann Arbor, MI 48109-2029. No postage-money or blank disks are necessary to get SIMLINK sent to you. SIMLINK may be available via anonymous FTP soon. For further information send email to boehnke@umich.edu. SIMLINK is now also available at the following URL http://www.sph.umich.edu/group/statgen/software. If you would like email notification of updates please send email to boehnke@umich.edu. SLINK: It is a Pascal program developed by D. Weeks, M. Lathrop, and J. Ott. It is similar to SIMLINK. It is more general than SIMLINK in that it allows for partial marker typing at the locus to be generated, but it runs slower than SIMLINK. It is available from linkage.cpmc.columbia.edu and watson.hgen.pitt.edu or on floppies (use the same address as for LINKAGE). 3.8) What programs are available to help detect errors in linkage data? [1995/11/30] Typically the linkage packages in and of themselves will detect errors in linkage data that are obvious, such as impossible phenotypes and genotypes, and obvious errors in pedigrees. Typically the programs will just grind to halt and allow you to fix the error, and try again until you finally succeed. However, errors that "make sense" to linkage programs will not be detected. GENO: It is a genotype entry/edit tool that will allow you to easily enter and manipulate genotyping data. You can also check the quality of your data with the built-in Mendelian inheritance checker. The author the of program is Matt Stephenson and can be reaced at stephenm@bioimage.mfldclin.edu. The program is available via FTP from dgabby.mfldclin.edu in /pub/geno. GENOCHECK: It 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. The author is Dr. Margaret Gelder Ehm the ftp site is at softlib.cs.rice.edu and it is in /pub/GenoCheck. It is written for Unix. 3.9) What programs help me recode genetic markers? [1995/03/01] DOLINK can downcode alleles automatically. However, the main use of DOLINK is to prepare files for LINKAGE from a database. In addition P. Adams package LABMAN and LINKMAN have features for the recoding of alleles. 4.0) LINKAGE PACKAGE SPECIFIC INFORMATION 4.1) How do I get my CEPH data into CRI-MAP format? [1995/03/01] You can output the file in linkage format and use link2gen in CRI-MAP. The disadvantage here is that your marker names are separated from your data and it's easy to make a mistake and get them mixed up. You can output the file in ped.out format and use CEPH2CRI mentioned above in the FAQ to do the conversion as well. 4.2) How do you calculate MAXHAP? [1995/09/09] MAXHAP is the maximum possible number of haplotypes in your analysis. You multiply together the number of alleles at each locus used in a particular run; not all loci in your dataset, just the loci you are using in that particular calculation. Remember that the affection status counts as two alleles, regardless of the number of liability classes. For example, if a dataset has the following information: the liability classes, marker A has 3 alleles, marker B has 4 alleles, and marker C has 5 alleles and your run includes a LINKMAP run between affection status, marker A, and marker B, then your MAXHAP must be at least 2*3*4=24. FASTLINK 2.3P includes an auxiliary program called ofm (optimize for maxhap) which can be used to automatically recompile the desired program with the ideal value of maxhap under the following assumptions: using UNIX or VMS (not DOS), running ILINK or LINKMAP or MLINK (not LODSCORE), the main script is produced by the LINKAGE auxiliary program LCP), and the locus file is produced by the LINKAGE auxiliary program PREPLINK; see README.ofm in the FASTLINK distribution. 4.3) When should you use binary coding instead of numeric allele coding? [1995/03/01] Usually there is no advantage to coding disease loci as either binary or numeric using liability classes. Generally, binary coding is more complex in that we humans often have a hard time thinking that way. Some of the codominant phenotypes lend themselves to binary coding; for example, ABO blood types: A (101), B (011), O (001), AB (111), and unknown (000). Since you cannot distinguish AO from AA at the phenotype level you code both genotypes as (101), presence of A and O. In reality O represents absence of both A and B. However, do not code using (000), since it would be an unknown. Use of binary codes has decreased since DNA markers have come into use since they allow one to type an individual with respect to genotype. You can use binary codes if you have phenotypic data which does not allow for the discrimination of the underlying genotype exactly, and one can code it as the presence with 1 or absence with 0 of factors such as the A and B antigens. Binary codes allow the representing loci with codominant and dominant mode of inheritance, while allele number notation is good only for codominant loci. Few people use binary factor notation. They either use allele numbers for codominant loci, or affection status notation for dominant loci. The main reason why binary factor notation is still currently used is that CEPH's database is in that notation. 4.4) What do you do when allele frequencies not add up to 1, for example, when alleles are not present in a pedigree under study? [1995/03/01] The best approach is to specify n+1 alleles, where there are n alleles actually observed in the pedigree. Use the correct allele frequencies for the n alleles, and for the n+1 allele, use 1 minus the sum of the frequencies of the observed alleles. 4.5) I use LINKAGE and/or FASTLINK, what references should I cite in my papers? [1995/03/01] FASTLINK users should cite: Cottingham, R. W. Jr., Idury, R. M., and Schaffer, A. A. "Faster Sequential Linkage Computations." American Journal of Human Genetics. 53:252-263, 1993. Schaffer, A. A. , Gupta, S. K., Shriram, K., and Cottingham, R. W. Jr. "Avoiding Recomputation in Linkage Analysis". Human Heredity. 44(4):225-37, 1994 Jul-Aug. In addition, all FASTLINK and LINKAGE users should also cite the LINKAGE papers: Lathrop, G.M., Lalouel, J.M., Julier, C. , and Ott, J. "Strategies for Multilocus Analysis in Humans." PNAS. 81:3443-3446, 1984. Lathrop, G.M. and Lalouel, J.M., "Easy Calculations of LOD Scores and Genetic Risks on Small Computers." American Journal of Human Genetics. 36:460-465, 1984. Lathrop, G.M., Lalouel, J.M., and R. L. White. "Construction of Human Linkage Maps: Likelihood Calculations for Multilocus Analysis." Genetic Epidemiology. 3:39-52, 1986. 4.6) What is recoding of alleles all about anyway? [1995/03/01] One of the problems with highly polymorphic markers is that they can increase the computational requirements of the computers by several orders of magnitude due to the large number of alleles present. This can put the computation of some lod scores out of reach for DOS computers and take many days on higher end systems. So it is important to use methods that reduce the number of alleles, and recoding will reduce the number of alleles in your calculations. The method of recoding of alleles described by J. Ott in the Annals of Human Genetics, 42:255-257 (1978) works very well, but can only be done when the mode of inheritance of the disease is known. An article inspired by Ott's original work written M. Braverman in Computers and Biomedical Research, 18:24-36 (1985) extends the recoding of alleles in two ways: 1) it allows for pedigrees of arbitrary structure, and 2) it allows for missing/partially known marker phenotypes. It is usually possible to recode marker alleles to some extent even if the mode of inheritance of the disease is not known since what is still desired with respect to the marker is a labeling which preserves the available information about the source of each marker allele. It is important, however, where the full ancestry of alleles cannot be traced in a pedigree, that the recoded alleles maintain the allele frequencies appropriate to the original alleles. In a complex disorder, this may not be possible. Another method is if the marker in question has 14 alleles in the general population, but only 9 alleles in the study population, it is possible to collapse the functional number of alleles to 9 or 10. Usually, adjust the allele frequencies to sum to 1 by dividing each allele frequency by the sum of the (observed) allele frequencies. For the latter all the allele frequencies remain the same, but the unobserved ones are collapsed into a single allele (and frequency). If there are 9 observed alleles (but there are 14 in the population), then rescaling the frequencies of the observed 9 alleles will also not produce quite correct results. Consider the unlikely example of a huge pedigree with only the most recent generation observed in which the observed 9 alleles all have very low and equal frequency. If there are distantly separated relatives who are affected there is some reasonable support for linkage since the alleles are rare. But if we rescale frequencies to 1/9 per alleles, then sharing of alleles isn't so unlikely. Coding the marker with 10 alleles produces correct results as it will produce the same lod scores as would coding the marker with 14 alleles. 4.7) What do you do when you get thetas greater than 0.5 when using LINKAGE? [1996/22/96] This seems to occur when the GEMINI optimization procedure prefers to go for a local optimum of a theta greater than 0.5 as a result of the starting theta values being to high in a LINKAGE run using ILINK or LODSCORE. This can easily be fixed by modifying the starting theta direclty with LCP or editing the LCP generated script. One can also modify the starting value with PREPLINK or by editing the data file containing allele and disease frequencies. This can be an iterative process and one should change theta values by an order of magnitude until reasonable thetas are obtained. One must also be careful of having intial thetas too low, this can also cause problems in the form of erroneous values. One can also run MLINK to examine what is happening at different thetas to determine the best starting theta. 5.0) COMPUTER ADMINISTRATION AND OPTIMIZATION 5.1) How can I increase the speed of the LINKAGE/FASTLINK package on my workstation? [1995/05/18] 1. Use FASTLINK, which is the C version of the LINKAGE package with a few algorithmic improvements. It can increase the speed of your calculations by an order of magnitude. 2. Setting up lots of paging space, which uses the hard drive as virtual memory (300 megs is usually plenty). Note that paging space is the same as swap space. Then use the "fast" versions of FASTLINK. 3. Use GCC, which is the GNU/Free Software Foundation C compiler, to compile FASTLINK. GCC produces machine language that is about 10% faster than Sun's C compiler. 4. Install the generic small kernel instead of the generic kernel. The generic kernel has device files for almost everything, and can slow the system down. The generic small kernel is configured for a system without many devices and without many users. Installing a generic small kernel is an option during system installation on Sun workstations. 5. Reconfigure your kernel so it has only devices you need. This should give you a small improvement in overall system speed, but if you are already running the generic-small kernel, additional improvement may be so small that it's not worth the trouble. If the generic small kernel is insufficient for your system this step is a must. The generic kernel will slow down your workstation significantly and most of the device support is unnecessary. 6. Don't run your linkage analyses in the background, because running programs in the background gives them a lower priority. Either do the runs in the foreground or you can use the root password to nice the pedin process by -3 to compensate (negative nice values give a higher priority). If you need to log out, you can use the screen command and "detach" a session so you can log out without programs terminating. Later you can log back in and "reattach" the session, which continued to run while you were logged out. The screen command is available at prep.ai.mit.edu and is also on the O'Reilly Unix Power Tools CD- ROM. According to the Sun documentation, nicing below -10 can interfere with the operating system and actually reduce the process' speed. Running them at the standard default level of 0 is usually sufficient. Some people recommend to run a background job to using nice +19 (!). In this way, the job will not interfere with other normal processes like login. 7. Runs with 100% penetrance can run faster than runs with incomplete penetrance. Of course, if you have an unaffected obligate carrier, this won't work. In addition, incomplete penetrance runs may be necessary for your research to be "good". 8. Change the block size of your file system. One can increase performance of a file system by increasing the block size, thus decreasing the number of read-write operations. A block device, such as a hard disk, usually accesses a block of data simultaneously. Thus, if one is expecting to use large files, having large blocks will be an advantage. However, one usually trades the number of bytes lost to partial files since one has to increase the fragment size to a number larger than 1024, for example 2048. That is, each file or part of a file occupies 2048 bytes, a file of 100 bytes will still occupy 2048 bytes. Therefore, bigger blocks give faster bigger blocks with bigger fragments and more lost space. 9. It has been noted that you can increase the speed of programs which create/access large files in the /tmp directory by creating a tmpfs file system. 10. Of course, buying more RAM will increase your speed. It's been said that increasing RAM from 16 to 32 megs will result in a large increase in speed and increasing RAM from 32-64 megs will result in a significant increase. However, increasing beyond 64 megs is not particularly helpful. 6.0) MOLECULAR BIOLOGY ISSUES IN LINKAGE ANALYSIS 6.1) What screening sets are available for linkage analysis? [1995/09/14] For humans there are the Weber lab screening sets: 3, 3A, 4, 4A, 5, 5A, and 6 . Primers for the markers within these sets are available from Research Genetics, both in unlabeled and fluorescent dye-conjugated forms. The information on these screening sets can be downloaded via FTP from dgabby.mfldclin.edu, they are in /pub. EOF From owner-gene-linkage@net.bio.net Thu Mar 14 22:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.gene-linkage Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 15 Mar 1996 02:10:25 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 149 Sender: daemon@net.bio.net Distribution: world Message-ID: <199603151001.CAA17729@net.bio.net> NNTP-Posting-Host: net.bio.net I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We have three sponsors to date with a couple more pending. The process is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we hope to have new and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Statistics are for the four week period from 22 Jan. - 18 Feb. 1996 and usage continues to grow. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5000 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 600 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. ---------------------------------------------------------------------- From owner-gene-linkage@net.bio.net Sat Mar 16 22:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!nntp.coast.net!howland.reston.ans.net!newsfeed.internetmci.com!netnews1.nwnet.net!news.u.washington.edu!toby From: toby@u.washington.edu ('Toby' H D Bradshaw) Newsgroups: bionet.molbio.gene-linkage Subject: Re: Software for haploid mapping Date: 17 Mar 1996 01:46:12 GMT Organization: University of Washington, Seattle Lines: 26 Message-ID: <4ifqt4$br8@nntp3.u.washington.edu> References: <4i9v3v$3rb@mozz.unh.edu> NNTP-Posting-Host: saul3.u.washington.edu NNTP-Posting-User: toby Try using MAPMAKER, encoding the marker genotypic data as a backcross. You'll also want to enter the data for each marker in both possible linkage phases. The conifer megagametophyte, zebrafish haploids, and some haplo-diploid insects have been done this way. -Toby Bradshaw toby@u.washington.edu In article <4i9v3v$3rb@mozz.unh.edu>, Thomas D. Kocher wrote: >We are generating haploid progeny from fish eggs using irradiated sperm >to activate development. The process is analogous to sperm-typing of >humans, except that we have much more DNA to work with. > >Now that we are generating tables of haploid genotypes, we need some >software to scan for linkages. Can anyone point me to some existing >software which could do the trick? > >Thomas D. Kocher >Assoc. Prof. >Dept. of Zoology >University of New Hampshire >Durham, NH 03824 From owner-gene-linkage@net.bio.net Sat Mar 16 22:00:00 1996 Path: biosci!UCRAC1.UCR.EDU!judelson From: judelson@UCRAC1.UCR.EDU (Howard S. Judelson) Newsgroups: bionet.molbio.gene-linkage Subject: postdoc positions: fungal genetics/map-based cloning/gene analysis Date: 17 Mar 1996 14:24:46 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 43 Sender: daemon@net.bio.net Distribution: world Message-ID: <199603172222.OAA07605@click.ucr.edu> NNTP-Posting-Host: net.bio.net POSTDOCTORAL POSITIONS Molecular genetics of the oomycete fungus, Phytophthora infestans Candidates are sought for two postdoctoral positions in a laboratory investing the molecular genetics of Phytophthora infestans, an oomycete fungus that causes the important late blight diseases of potato and tomato. Successful applicants can join either of several on-going projects. These include the positional cloning of genes determining mating type (sexual compatibility type; see Judelson et al. 1995, Genetics 141:503-512); the analysis of genome rearrangements associated with a system of balanced lethals in Phytophthora; the characterization of mating-induced genes (isolated by differential display and subtraction cloning); and the analysis of genes determining resistance to fungicides. Major funding for these positions comes from grants from the USDA and NSF. Applicants should have a Ph.D. and some experience in molecular biology. Depending on the project, the experiments will involve techniques such as genetic mapping, long-range restriction mapping, chromosome walking in cosmid and BAC libraries, and fungal transformation; experience with these would be helpful but is not required. Please sent a curriculum vitae and the names of three references (including addresses and telephone numbers) to: Howard Judelson Department of Plant Pathology University of California Riverside, California 92521 USA email: judelson@ucrac1.ucr.edu fax: 909-787-4294 Howard Judelson (judelson@ucrac1.ucr.edu) Assistant Professor Department of Plant Pathology University of California Riverside, California 92521 USA Tel: 909-787-4199 Fax: 909-787-4294 From owner-gene-linkage@net.bio.net Sun Mar 17 22:00:00 1996 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!chi-news.cic.net!news.newnorth.net!news From: Craig Echt Newsgroups: bionet.molbio.gene-linkage Subject: Re: Software for haploid mapping Date: Mon, 18 Mar 1996 10:54:14 -0600 Organization: USDA Forest Service Lines: 25 Message-ID: <314D9536.6630@newnorth.net> Reply-To: cecht@newnorth.net NNTP-Posting-Host: rhin-cs-13.newnorth.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; PPC) To add to Dr. Bradshaw's sage advice, a detailed description of the use of MAPMAKER for haploid linkage analysis can be found in: Plomion et al. (1995) Genomic analysis in maritime pine (Pinus pinaster). Comparison of two RAPD maps using selfed and open-pollinated seeds of the same individual. Theor Appl Genet 90:1028-1034. ===================================== Craig S. Echt Research Geneticist, USDA Forest Service Forestry Sciences Lab e-mail: cecht@newnorth.net 5985 County Rd. K Ph: (715) 362-1114 Rhinelander, WI 54501 fax: (715) 362-1166 USA -------------------------------- 'Toby' H D Bradshaw wrote: > > Try using MAPMAKER, encoding the marker genotypic data as > a backcross. You'll also want to enter the data for each > marker in both possible linkage phases. The conifer megagametophyte, > zebrafish haploids, and some haplo-diploid insects have been done > this way. > > -Toby Bradshaw > toby@u.washington.edu > From owner-gene-linkage@net.bio.net Mon Mar 18 22:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!swrinde!sgigate.sgi.com!nntp.coast.net!swidir.switch.ch!in2p3.fr!univ-lyon1.fr!news From: 4BC Newsgroups: bionet.molbio.gene-linkage Subject: help RETROTRANSPOSONS Date: 19 Mar 1996 18:44:59 GMT Organization: insa-lyon.fr Lines: 9 Message-ID: <4imvbb$g74@tempo.univ-lyon1.fr> NNTP-Posting-Host: pc406-07.insa-lyon.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) I'm studiing biology in INSA lyon in France and I'm looking for informations on retrotransposons to make a presentation in my course of genetic of micro-organisms. If you know some good references, synthtetic, easy to understand book or paper, would you please email me. Thank you in advance Eric From owner-gene-linkage@net.bio.net Tue Mar 19 22:00:00 1996 Path: biosci!rutgers!uwm.edu!newsfeed.internetmci.com!swrinde!tank.news.pipex.net!pipex!warwick!bham!bhamcs!news.ox.ac.uk!newton!dan From: "Daniel E. Weeks" Newsgroups: bionet.molbio.gene-linkage Subject: Wellcome Trust Summer School: Genetic Analysis Date: Wed, 20 Mar 1996 12:30:48 +0000 Organization: Oxford University Lines: 98 Message-ID: NNTP-Posting-Host: newton.well.ox.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: QUOTED-PRINTABLE X-Sender: dan@newton WELLCOME TRUST SUMMER SCHOOLS SEVENTEENTH ADVANCED COURSE HUMAN GENOME ANALYSIS: GENETIC ANALYSIS OF MULTIFACTORIAL DISEASES 21st - 26th July 1996 The Wellcome Trust Centre for Human Genetics, University of Oxford=20 Windmill Road, Headington, Oxford, OX3 7BN An intensive computer-based course aimed at scientists actively involved in genetic analysis of multifactorial traits.=20 Programme For each of the following areas, we will discuss issues of power to detect linkage, optimal study design, use of software, and proper statistical analyses:=20 1.=09Qualitative traits: sib-pair methods 2.=09Qualtitative traits: affected-relative methods 3.=09Quantitative traits: sib-pair methods 4.=09Quantitative traits: regressive models 5.=09Linkage disequilibrium: testing for association Teaching will take the form of lectures by invited speakers, informal tutorials, hands-on computer sessions and analysis of disease family data sets. There will also be an opportunity to analyse and discuss participants' own data sets.=20 Course Organisers DANIEL WEEKS, MARK LATHROP. Confirmed speakers include: CHRIS AMOS (Houston), DAVID GOLDGAR (Utah), ADRIAN HILL (Oxford), SUN-WEI GUO (Ann Arbor), PETER HOLMANS (Cardiff), ELLEN WIJSMAN (Seattle).=20 Participants Applicants should be scientists at an advanced level of research (post-doctoral or equivalent). Documentation verifying that the applicant is actively engaged in a linkage or family-based association study (animal/human) must be provided with the applica tion. The course is subsidised by the Wellcome Trust for scientists based in academic institutions anywhere in the world. This is a residential course, without exception, and there is a charge of =9C350 pounds towards board and lodging= .=20 Applications There are no formal application forms, but applicants should send a hard copy of their full CV together with a 300 word outline of their current and ongoing research plans, indicating the relevance of the course, to Dr Pelin Faik, Course Co-ordinator, Div ision of Biochemistry & Molecular Biology, UMDS, Guy's Campus, London Bridge SE1 9RT. Notification of places will be in May. Further information on http://www.umds.ac.uk/wlmg.=20 Tel: 0171 403 6998=0DFax: 0171 407 5281=0DEmail: wss@umds.ac.uk Closing date for applications is 29th March 1996 ________________________________________________________________________ COURSE SUMMARY For each of the following areas, we will discuss issues of power to detect linkage, optimal study design, use of software, and proper statistical analyses:=20 1 =09Qualitative traits: sib-pair methods Comparison of identity-by-descent, identity-by-state and maximum likelihood methods of affected sib-pair analysis.=20 2 Qualitative traits: affected-relative methods General non-parametric tests aimed at detecting linkage by testing for increased marker similarity between the affected members of a pedigree.=20 3 Quantitative traits: sib-pair methods Comparison of different methods, including the Haseman-Elston least-squares regression procedure, variance components methods, and multilocus approaches.=20 4 Quantitative traits: regressive models How to model familial correlations in the presence of major gene effects and other sources of familial correlations.=20 5 Linkage disequilibrium: testing for association =20 Use of tests for linkage disequilibrium between markers and disease, including the haplotype relative risk (HHR) and transmission/disequilibirium (TDT) tests.=20 From owner-gene-linkage@net.bio.net Sun Mar 24 22:00:00 1996 Path: biosci!agate!usenet.kornet.nm.kr!news.kreonet.re.kr!news.dacom.co.kr!nntp.coast.net!howland.reston.ans.net!univ-lyon1.fr!news From: Olivier Champoussin Newsgroups: bionet.molbio.gene-linkage,bionet.general,fr.rec.genealogie,fr.bio.general Subject: The SF1 gene ...... Where? Date: 25 Mar 1996 09:39:30 GMT Organization: LAI - INSA de lyon Lines: 22 Message-ID: <4j5pki$lju@tempo.univ-lyon1.fr> NNTP-Posting-Host: laipc1.insa-lyon.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) Xref: biosci bionet.molbio.gene-linkage:1017 bionet.general:20679 Excuse me I'm a PhD studient in robotics. But one of my friend ask me about information I can catch from the net about a gene (SF1). did some one have information about SF1 or where I can find it. Tanks Sincerely olivier CHAMPOUSSIN ------------------------------------------------- INSA de Lyon F-69621 Villeurbanne Cedex (France) (33) 72-43-87-40 fax (33) 72-43-85-35 e-mail champou@lai1.insa-lyon.fr From owner-gene-linkage@net.bio.net Sun Mar 24 22:00:00 1996 Path: biosci!agate!usenet.kornet.nm.kr!news.kreonet.re.kr!usenet.seri.re.kr!news.dacom.co.kr!nntp.coast.net!howland.reston.ans.net!univ-lyon1.fr!news From: Olivier Champoussin Newsgroups: bionet.molbio.gene-linkage,bionet.general,fr.rec.genealogie,fr.bio.general Subject: (no subject) Date: 25 Mar 1996 09:39:17 GMT Organization: LAI - INSA de lyon Lines: 22 Message-ID: <4j5pk5$lju@tempo.univ-lyon1.fr> NNTP-Posting-Host: laipc1.insa-lyon.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) To: The,SF1,gene,......,Where? Xref: biosci bionet.molbio.gene-linkage:1016 bionet.general:20678 Excuse me I'm a PhD studient in robotics. But one of my friend ask me about information I can catch from the net about a gene (SF1). did some one have information about SF1 or where I can find it. Tanks Sincerely olivier CHAMPOUSSIN ------------------------------------------------- INSA de Lyon F-69621 Villeurbanne Cedex (France) (33) 72-43-87-40 fax (33) 72-43-85-35 e-mail champou@lai1.insa-lyon.fr From owner-gene-linkage@net.bio.net Tue Mar 26 22:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!howland.reston.ans.net!math.ohio-state.edu!jussieu.fr!pasteur.fr!univ-lyon1.fr!news From: 4BC Newsgroups: bionet.molbio.gene-linkage Subject: (no subject) Date: 27 Mar 1996 13:14:02 GMT Organization: insa-lyon.fr Lines: 16 Message-ID: <4jbeuq$5iv@tempo.univ-lyon1.fr> NNTP-Posting-Host: pc406-07.insa-lyon.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) Hello I'm a french student from INSA : a school engeneering and I'm looking forward some articles about oncogenes and prooncogenes and antioncogenes. If this newsgroup is not able to answer me , could you please indicate me the best newsgroup to subscribe to have information about this topic. Thank you very much Isabelle MUNARI Ps: could you precise in the subject that the mail is for ISA M...Thank you From owner-gene-linkage@net.bio.net Wed Mar 27 22:00:00 1996 Newsgroups: bionet.molbio.gene-linkage Path: biosci!ihnp4.ucsd.edu!agate!news.Stanford.EDU!nntp-hub2.barrnet.net!sgigate.sgi.com!nntp.coast.net!howland.reston.ans.net!newsfeed.internetmci.com!in1.uu.net!EU.net!ieunet!news.tcd.ie!cmegan.gen.tcd.ie!user From: dmachugh@mail.tcd.ie (David MacHugh) Subject: Linkage disequilibrium & Haplotypes Message-ID: Sender: usenet@news.tcd.ie (TCD News System ) Organization: Genetics Department, Trinity College, Dublin 2 Date: Thu, 28 Mar 1996 13:25:54 GMT Lines: 36 Hi, I have a query about using the GENEPOP program (Raymond & Rousset [1995] J. Hered. 86(3): 248-49). We have haplotypic data from a number of microsatellites typed in human males on the X-chromosome. Basically we would like to determine the extent of linkage disequilibrium among these markers (STRs) using the GENEPOP program. Does anyone know of any theoretical objections to recoding the data as pseudo-homozygotes and testing for LD? Perhaps someone might know a more appropriate method for dealing with this type of data. Data format: Individual 1: 120 145 130 210 151 Individual 2: 122 143 134 208 157 etc. Thanks in advance, David MacHugh, Genetics Department, Trinity College, Dublin 2. IRELAND. E-mail: dmachugh@mail.tcd.ie From owner-gene-linkage@net.bio.net Wed Mar 27 22:00:00 1996 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!ulcc.ac.uk!usenet From: dcurtis@hgmp.mrc.ac.uk (Dave Curtis) Newsgroups: bionet.molbio.gene-linkage Subject: Re: Linkage disequilibrium & Haplotypes Date: Fri, 29 Mar 1996 05:29:06 GMT Organization: University of London Computer Centre Lines: 23 Message-ID: <4jf09m$moa@calypso.ulcc.ac.uk> References: NNTP-Posting-Host: ezdu053.ds.ulcc.ac.uk X-Newsreader: Forte Free Agent 1.0.82 dmachugh@mail.tcd.ie (David MacHugh) wrote: >We have haplotypic data from a number of microsatellites typed in human >males on the X-chromosome. >Basically we would like to determine the extent of linkage disequilibrium >among these markers (STRs) using the GENEPOP program. >Does anyone know of any theoretical objections to recoding the data as >pseudo-homozygotes and testing for LD? This sounds to me like it must tbe wrong - you're treating each observation as if it were two observations. >Perhaps someone might know a more appropriate method for dealing with this >type of data. I could think about it. Are you talking about examining each pair of loci separately, or a group together? Dave Curtis http://www.gene.ucl.ac.uk/~dcurtis