Linkage Analysis of Pedigrees with Loops
bachner at Cassini.genethon.fr
Fri Jun 30 09:49:14 EST 1995
Gregory M. Acland wrote
I would appreciate advice from anyone with insight or experience into
analysing pedigrees with multiple loops. I understand, from discussions at
Dr Ott's introductory course on Linkage Analysis, that the Linkage package
can be recompiled with the Maxloops constant set at a desired number other
than the default.
How severe are the trade offs?
The pedigrees involved are canine, and do not have huge numbers of
individuals. Probably somewhere in the order of 30 to 50 individuals per
family. The loops are unavoidable, however, as they are prexisting rather
than planned pedigrees. Something like 6 to 10 loops per pedigree is
Does changing Maxloops to something like 10 increase the compute time
drastically for pedigrees of this sort of size?
I am currently running the Linkage package on a DOS machine (100 Mhz 486,
16 MB RAM), and don't have ready access to a Unix system.
What source programs do I need to compile to yield a version of the Linkage
package customized to deal with this many loops. What are the current
versions that should be used? Is Borland Turbo/Pascal still the compiler of
choice? Are there other compile options that should be considered at the
Alternatively, can Fastlink deal with loops at all, and if so, can it deal
with this many loops. If so, can I obtain a DOS-executable version with
the capacity to handle this many loops?
Gregory M. Acland (607) 256-5684
Center for Canine Genetics & Reproduction (607) 256-5689 [fax]
James A. Baker Institute for Animal Health gma2 at cornell.edu
College of Veterinary Medicine
Hungerford Hill Rd, Ithaca, New York 14853
My opinion, mainly heuristic but based on experience is that you have
no chance to run that kind of problems on a DOS machine even with fastlink
mainly because you will need a huge amount of RAM.
Moreover if you manage this first problem, anyway the run on DOS machines is likely to take
many months or years or maybe centuries.
As I'm beginning to manage a linkage server at INFOBIOGEN (France) I can try
to run your problem on powerful Unix machines.
If interested I just need the raw files, description of loops or pedigree drawings
and what kind of results you want.
(If I succeed I only ask you to quote INFOBIOGEN in Methods section of paper)
For any further infos about this topic please mail to
linkage at infobiogen.fr
Laboratoire de Biochimie Genetique,Hopital Cochin.
123 Bd. Port Royal, 75014 Paris, France.
Tel: (33 1) 42-34-12-12 ext 3039 FAX: (33 1) 44-41-15-22
e-mail : bachner at Cassini.genethon.fr
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