Navigating Public Physical Mapping Databases

Lincoln D. Stein1

1 Whitehead Institute/MIT Center for Genome Research, Cambridge, Massachusetts
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 5.16
DOI:  10.1002/0471142905.hg0516s13
Online Posting Date:  May, 2001
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

Abstract

This unit provides concise overviews of the many physical mapping resources available and relates them to the genetic and transcript maps. Useful information on resolution of the maps, how to access them, and how to interpret them is compiled and presented in a clear fashion. Especially useful is a set of detailed protocols describing how to construct an STS marker and how to map it by means of available yeast artificial chromosomes (YACs). An additional protocol describes accessing EST marker maps.

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Types of Physical Maps
  • Genome‐Wide Maps from Large Community Databases
  • Basic Protocol 1: Navigating Chromosome Maps in NCBI Entrez
  • Basic Protocol 2: Navigating Chromosome Maps in GDB
  • Genome‐Wide Maps from Individual Sources
  • Basic Protocol 3: Browsing the NCBI Transcript Map
  • Basic Protocol 4: Creating an STS for Placement on the Whitehead Maps
  • Basic Protocol 5: Mapping an STS Relative to the Whitehead STS/YAC Content Map
  • Basic Protocol 6: Retrieving YAC Overlap from the CEPH Server
  • Chromosome‐Specific Maps
  • Figures
  • Tables
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

Literature Cited
   Adams, M.D., Kelley, J.M., Gocayne, J.D., Dubnick, M., Polymeropoulos, M.H., Xiao, H., Merril, C.R., Wu, A., Olde, B., Moreno, R.F., Kerlavage, A.R., McCombie, W.R., and Venter, J.C. 1991. Complementary DNA sequencing: Expressed sequence tags and human genome project. Science 252:1651‐1656.
   Anuff, E. 1995. Java Sourcebook. John Wiley & Sons, New York.
   Boguski, M., Tolstoshev, C.M., and Bassett, D.E. 1994. Gene discovery in dbEST. Science 165:1993‐1994 (letter).
   Bell, C.J., Budarf, M.L., Nieuwenhuijsen, B.W., Barnowski, B.L., Buetow, K.H., Campbell, K., Colbert, A.M.E., Collins, J., Daly, M., Desjardins, P.R., DeZwaan, T., Eckman, B., Foote, S., Hart, K., Hiester, K., Van Het Hoog, M.J., Hopper, E., Kaufman, A., McDermid, H.E., Overton, G.C., Reeve, M.P., Searls, D.B., Stein, L., Valmiki, V.H., Watson, E., Williams, S., Winston, R., Nussbaum, R.L., Lander, E.S., Fischbeck, K.H., Emanuel, B.S., and Hudson, T.J. 1995. Integration of physical, breakpoint and genetic maps of chromosome 22: Localization of 587 yeast artificial chromosomes with 238 mapped markers. Hum. Mol. Genet. 4:59‐69.
   Chumakov, I., Rigault, P., Le Gall, I., et al., and Cohen, D. 1995. A YAC contig map of the human genome. Nature 377(Suppl.):174‐297.
   Cohen, D., Chumakov, I., and Weissenbach, J. 1993. A first generation physical map of the human genome. Nature 336:698‐701.
   Cox, D. 1992. Radiation hybrid mapping. Cytogenet. Cell Genet. 59:80‐81.
   Dib, C., Faure, S., Fizames, C., Samson, D., Drou, N., Vignal, A., Millasseau, P., Marc, S., Hazan, J., Seboun, E., Lathrop, M., Gyapay, G., Morissette, J., and Weissenbach, J. 1996. A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380:152‐154.
   Doggett, N.A., Goodwin, L.A., Tesmer, J.G., Meincke, L.J., Bruce, D.C., Clark, L.M., Altherr, M.R., Ford, A.A., Chi, H.‐C., Marrone, B.L., Longmire, J.L., Lane, S.A., Whitmore, S.A., Lowenstein, M.G., Sutherland, R.D., Mundt, M.O., Knill, E.H., Bruno, W.J., Macken, C.A., Torney, D.C., Wu, J.‐R., Griffith, J., Sutherland, G.R., Deaven, L.L., Callen, D.F., and Moyzis, R.K. 1995. An integrated physical map of human chromosome 16. Nature 377(Suppl.):335‐365.
   Hillier, L., Lennon, G., Becker, M., Bonaldo, M., Chiapelli, Chissoe, S., Dietrich, N., DuBuque, T., Favello, A., Gish, W., Hawkins, M., Hultman, M., Kucaba, T., Lacy, M., Le, M., Le, N., Mardis, E., Moore, B., Morris, M., Parsons, J., Prange, C., Rifkin, L., Rohlfing, T., Schellenberg, K., Soares, M.B., Tan, F., Thierry‐Meg, J., Trevaskis, E., Underwood, K., Wohldman, P., Waterston, R., Wilson, R., and Marra, M. 1996. Generation and analysis of 280,000 human expressed sequence tags. Genome Res. 6:807‐828.
   Houlgatte, R., Mariage‐Samson, R., Duprat, S., Tessier, A., Bentolila, W., Lamy, B., and Auffray, C. 1995. The Genexpress Index: A resource for gene discovery and the genic map of the human genome. Genome Res. 5:272‐304.
   Hudson, T.J., Stein, L.D., Gerety, S. S., Ma, J., et al., and Lander, E.S. 1995. An STS‐based map of the human genome. Science 270:1945‐1954.
   Kogelnik, A.M., Lott, M.T., Brown, M.D., Navathe, S.B., and Wallace, D.C. 1996. MITOMAP: A human mitochondrial genome database. Nucl. Acids Res. 24:177‐179.
   Lichter, P.C., Tang, J., Call, K., Hermanson, G., Evans, G., Housman, A.D., and Ward, D.C. 1990. High resolution mapping of human chromosome 11 by in situ hybridization with cosmid clones. Science 247:64‐68.
   Marynen, P. and Kucherlapati, R. 1995. Report of the Third International Workshop on Human Chromosome 12 Mapping. Cytogenet. Cell Genet. 73:1‐24.
   Murray, J.C., Buetow, K.H., Weber, J.L., Ludwigsen, S., Scherpbier‐Heddema, Manion,T.F., Quillen, J., Sheffield, V.C., Sunden, S., and Duyk, G.M. 1994. A comprehensive human linkage map with centimorgan density: Cooperative Human Linkage Center (CHLC). Science 65:2049‐2054.
   O'Connell, P., Leach, R.J., Rains, D., Taylor, T., Garcia, D., Ballard, L., Holik, P., Weissenbach, J., Sherman, S., Wilkie, P., Weber, J.L., and Naylor, S.L. 1996. A PCR‐based genetic map for human chromosome 3. Genomics 24:557‐567.
   Schuler, G.D., Boguski, M.S., Stewart, E.A., Stein, L.D., et al., and Hudson, T.J. 1996. A gene map of the human genome. Science 274:540‐546.
   Vollrath, D., Foote, S., Hilton, A., Brown, L.G., Beer‐Romero, P., Bogan, J.S., and Page, D.C. 1992. The human Y chromosome: A 43‐interval map based on naturally occurring deletions. Science 258:52‐59.
Internet Resources
   lirmm.lirmm.fr
  Anonymous FTP servers for C. elegans database (ACEDB) developed by R. Durbin and J. Thierry‐Mieg: documentation, code and data.
   cele.mrc‐lmb.cam.ac.uk
  Full text of WWW Entrez: A hypertext retrieval tool for molecular biology. J.A. Epstein, J.A. Kans, and G.D. Schuler; Second International World Wide Web Conference Chicago, Illinois, 1994.
   ncbi.nlm.nih.gov
  Code available for Primer 3, S. Rozen. and H.J. Skaletsky, (1996)/.
   http://www3.ncbi.nlm.nih.gov/WWW2/WWW2_paper2.html
  http://www‐genome.wi.mit.edu/genome_software/other/primer3.html
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library