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遗传连锁分析常用网络资源:Genotyping&Linkage Analysis WWW links  

2011-12-05 13:59:31|  分类: 数量遗传学 |  标签: |举报 |字号 订阅

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Marker lists

(If you have trouble downloading these with your browser, try right-clicking and saving the link directly.)
  • A spreadsheet I put together listing all ABI dye-labeled markers, in all 80-odd panels, arranged by Marshfield map position. Also includes info on size range and dye. Useful when ordering new markers to cover an interesting region. Created May, 2001; may be somewhat outdated. Order individual markers from www.appliedbiosystems.com, P/N 4329191, $52.50/tube (300 rxns), "Human Linkage Mapping v2.5 Primer Pairs". Specify chromosome, panel, and marker name.
  • My spreadsheet listing markers that can be ordered from ResGen, sorted by Marshfield map position. Created September 2000; may be somewhat outdated. Double-check before ordering at www.resgen.com.

allele frequencies


References to use for linkage analysis software

We currently use version 4.0P of FASTLINK along with version 5.1 of the LINKAGE package. (These run transparently under mlinker.) For multipoint analysis, we use version 1.0 of Vitesse.

    For LINKAGE:
  • G. M. Lathrop, J.-M. Lalouel, C. Julier, and J. Ott, Strategies for Multilocus Analysis in Humans, PNAS 81(1984), pp. 3443-3446.
  • G. M. Lathrop and J.-M. Lalouel, Easy Calculations of LOD Scores and Genetic Risks on Small Computers, American Journal of Human Genetics, 36(1984), pp. 460-465.
  • G. M. Lathrop, J.-M. Lalouel, and R. L. White, Construction of Human Genetic Linkage Maps: Likelihood Calculations for Multilocus Analysis, Genetic Epidemiology 3(1986), pp. 39-52.
    For Fastlink:
  • R. W. Cottingham Jr., R. M. Idury, and A. A. Schaffer, Faster Sequential Genetic Linkage Computations, American Journal of Human Genetics, 53(1993), pp. 252-263. (PDF)
  • A. A. Schaffer, S. K. Gupta, K. Shriram, and R. W. Cottingham, Jr., Avoiding Recomputation in Linkage Analysis, Human Heredity, 44(1994), pp. 225-237.
  • (PDF)
    For Vitesse:
  • O'Connell JR, Weeks DE. The VITESSE algorithm for rapid exact multilocus linkage analysis via genotype set-recoding and fuzzy inheritance. Nat Genet. 1995. 11:402-8.
    For Pedcheck:
  • O'Connell JR, Weeks DE, PedCheck: A program for identifying genotype incompatibilities in linkage analysis, Am J Hum Genet 63:259-266
    For Molscript and Raster3D (protein-model-drawing software):
  • Kraulis, Per J., "MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures", Journal of Applied Crystallography (1991) vol 24, pp 946-950.
  • Merritt, Ethan A. and Bacon, David J. (1997). "Raster3D: Photorealistic Molecular Graphics" Methods in Enzymology 277, 505-524.

Steve DePalma | depalma at rascal.med.harvard | http://genetics.med.harvard.edu/~depalma
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