• What is RH Map Server?
• How do I use RH Map Server?
• What other information can I get to via RH Map Server?
• What do the RH Map Server results look like?
• Let me use RH Map Server...

RH Map Sever is an interactive program for placing markers on the current MCW Radiation Hybrid framework map. Users can submit RH vectors from their own mapping experiments and the tool will attempt to place them on the MCW map. RH Map Server is based on rhmapper by Lincoln Stein and uses a hidden Markov model for maximum likelihood calculations on multipoint maps.

Reference information:

• MCW RH Map - Steen RG, Kwitek-Black AE, et al., Genome Research, 1999, 6:1-8
• RHMapper - L. Stein, L. Kruglyak, D. Slonim and E. Lander. (1995) RHMAPPER, unpublished software, Whitehead Institute/MIT Center for Genome Research

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1. Either upload your RH Vector data from a file or paste the RH Vector data into the indicated text field
   
   Vectors should be 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.
   
2. Click Submit Vectors
3. A summary of your vectors is returned and you have three additional fields to check:
   
   
   
   1. Enter your email address so the results can be emailed to you when they are complete.
   2. Review your submitted vectors, you can deselect any which you do not wish to place (you may decided there are too many '2's (unknown scores) or too many '1's to get a decent placement)
   3. Enter a LOD cutoff value for the placement. This is the threshold the application uses to place your marker(s). Markers are placed at that cutoff value and results returned if the confidence in the marker's position (measured by a LOD score) is at or above the cutoff value. If markers fail to place at a given LOD cutoff, lowering the value will increase the chance of placement but also reduce the confidence in the position returned.
      
      
4. Click Run RH Placement to submit the vectors to the map server.

You will be notified by email when the placement is complete and you can then return to check the results.

Data Management Policy

• No copies are kept of either your submitted vectors or your placement results
• Your results will only be available online for a total of THREE days. Please check your results as soon as you receive your email notification to ensure that you can take advantage of your submissions.
• You may also delete your data yourself through our online service.

You can give the RH Mapserver a try by pasting in the sample RH vectors shown above for Aldoa, atp1a3, etc. into the form.

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The current MCW RH map is available in the Maps section of RGD.

The dataset listing all the mapped markers, their placement LOD and the primer and clone sequences is available MAPS_DATA file on the FTP site.

The RHMapper software is available from the Whitehead Institute

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You will be notified by email when the results are available. The email contains a summary of the results plus a link to the complete online result page. The online results will list the following options:

Graphical images are available in the Maps (gif) section, a section of a map is shown below. Click to view the entire map.

Data is automatically removed from the server after three days and no copies are retained, however, you can manually delete you datasets using the DELETE option on the results page.

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