Rat RH Map Server

This tool will run RHMAPPER [1] and create a RH placement map of your submitted RH Vectors based on the 1999 RH Framework of the Rat [2].

RH Map Server submission instructions

1. Either upload your RH Vector data from a file or paste the RH Vector data into the indicated text field. The vector data should be in the appropriate data format, described below.
2. The RH Mapserver will check your submitted vectors and then allow you to choose which should go forward for placement against the framework maps.
3. Submitted vectors will be placed against the framework maps in batch mode, when the results are available you will receive email notification indicating where your results can be obtained.

   Click here for more help.

RH Vector Notes

• The Rat Radiation Hybrid Panel is a 106 hybrid panel. More information is available from Research Genetics.
• The Rat RH framework was generated using hybrids 1 through 100.
• The RH vectors should consist of 0's, 1', or 2's from hybrids # 1-106 in that order. If you have missed hybrids, please add 2's for those missing hybrids.
• In the rhvectors, 0 represents negative, 1 positive and 2 ambiguous or missing data.
• If you have vectors with length shorter than 106, the tool will add 2's at the end of your vector.
• Data Format - The data should be arranged in the following format:
  
  

  aldoa   0000000210000000000000001000000000010020000010000000001010100110001012100010000021011101000100222222
  atp1a3  0010000010000000000001100010000000000000000010000001001001000200100001010000000011010011000101222222
  atp4a   0001000100000000000001120010200000000000000000000001001000000110100010010000000011010001000201222222
  cgrat10 2011101010000001110201100000000000210210000010101121001100120000001000110001201100000020020000010001
      

  The first column is the marker name which is limited to 11 characters, the second is the rhvector string, any remaining columns will be discarded, Each column is delimited by a tab, space or comma.

References

1. L. Stein, L. Kruglyak, D. Slonim and E. Lander. (1995) RHMAPPER, unpublished software,Whitehead Institute/MIT Center for Genome Research.
2. Robert G. Steen, Anne E. Kwitek-Black, Christopher Glenn, Jo Gullings-Handley, William Van Etten, O. Scott Atkinson, Diane Appel, Simon Twigger, Melanie Muir, Tim Mull, Mary Granados, Mushira Kissebah, Kerri Russo, Robbin Crane, Michael Popp, Marc Peden, Tara Matise, Donna M.Brown, Jian Lu, Stephen Kingsmore, Peter J. Tonellato, Steve Rozen, Donna Slonim, Peter Young, Margit Knoblauch, Abraham Provoost, Detlev Ganten, Steven D. Colman, Jonathan Rothberg, Eric S.Lander, and Howard J. Jacob, A High Density Integrated Genetic and Radiation Hybrid Map of the Laboratory Rat, Genome Research 1999, May.