[LOGO]Radiation Hybrid Mapping

Introduction

This form allows you to map STSs relative to the Whitehead Institute/MIT Center for Genome Research's radiation hybrid map of the human genome. Enter the radiation hybrid screening results for your STSs here. At regular intervals a software program will assign your STSs to chromosomes and find their best positions on the framework maps. The results will be mailed back to you, usually within an hour.

Please see the instructions before proceeding, including details about the LOD scores displayed with the results.

Your e-mail address (used to send the results back to you!). Change this to your correct address:

Paste in screening data formatted as described in the instructions:

Alternative, indicate a data file to upload (Netscape 2.0 or greater):

Data format:

LOD score for linkage:

Return diagrams of the mapped markers as:


Instructions

To use this service, follow these instructions carefully.
  1. Screen your STSs by PCR on the Genebridge4 Radiation Hybrid screening panel. This panel is available through Research Genetics.
  2. Format the screening results as a vector of 0's and 1's. Unknown/uncertain data should be indicated with dashes (-) or 2's. You may use spaces to improve readability, but this isn't necessary
  3. Using the popup menu, select an order for the hybrids in the data vector you provide. This server supports two different orders:
    1. The official Genebridge4 order, in which all 93 hybrids are arranged in alphabetic order.
    2. The abbreviated Whitehead order, which uses only 91 hybrids arranged in a slightly different order.
    For consistency of comparison, we suggest you use the official order.
  4. Arrange the results in a table: STS name first and then the data vector. Here is an example (not all 91 cell lines shown): 
           HK45-L 01110 10112 00111 01011 01101 00101 01011 11100
       MBQH2  01100 02000 00000 11111 01111 00100 11200 01010
       Glue2  11110 01110 10010 10011 01010 01110 11200 11010
  5. Enter your correct e-mail address in the space provided, then cut and paste the data table into the text field. Alternatively, if you have a Netscape (2.0 or greater) browser, you may save the data into a ASCII (text only) file, and use the "upload a file" field to transmit it. Please don't attempt to upload a binary file, such as a "Normal format" Microsoft Word or Excel file. The software on this end can't read those formats.
  6. If you wish to receive a picture of the mapped markers, check either the "Macintosh picture" or "GIF" checkboxes. These are the only formats we support currently. Your mailer must be able to handle enclosures for this to work successfully. If you select "Macintosh picture", you will receive a BinHex'd PICT file (most mail programs recognize and deal with BinHex automatically). If you select "GIF", you will receive a uuencoded enclosure (most PC mail programs recognize and deal with this format successfully, Unix users should be able to figure it out for themselves).
  7. By default, the pictures returned will show your markers in the context of the high-likelihood framework map. If you check the Return placement map checkbox, you will get the entire map for the chromosome, including markers that are placed at low odds ratios. Warning: the pictures returned with this option can be quite large!
  8. Select the LOD score for linkage to the framework map. Because of the large size of the framework map, you need to set a high LOD in order to avoid spurious linkage. 15 is recommended for a first pass. If you find no linkage, try it with a lower threshold.
  9. Press the "Submit" button. If all looks satisfactory, you will receive an acknowledgement. Usually within an hour, you will receive the mapping results by e-mail.
  10. Note about pictures: if the marker is not mapped to only one chromosome, requested pictures will not be generated. If this happens, increase the LOD score cutoff and resubmit. If the marker does not map to any chromosomes, try reducing the LOD score cutoff and resubmitting.
  11. The results should look something like this if the marker only maps to one chromosome: 
    NAME            Chromosomal Assignment and Placement(s)
----            ---------------------------------------
markername      Chromosome Chr8
                Places 1.2 cR from WI-4688
                Places 12.12 cR from WI-6536 (lod 1.46 relative to most likely)
                Places 15.0 cR from WI-961 (lod 2.62 relative to most likely)
    The marker will also be displayed in the context of the framework below, as below: 
    Name             Dist   Type   Vector
----             ----   ----   ------
WI-9262          15.1   F      000100010100100000000000010110010000001001000110001000000000011001001111011000002102100000211
CHLC.GATA72C10   7.8    F      002100010100100000100010010110010001001201001110101000000000011001001111011011001102111000211
WI-5962          4.9    F      000100010100100000000010010111010001001001001110101000000000011001001111011000001102101000211
D8S280           8.1    F      000100010100100000000010110111012001001001001110101000000000011001001211011002001102000000211
WI-4688          9.2    F      000100010100100000000000110112000001001001000110001000000000011001001101011000001202000000211
markername       1.2    P1.2   000100010100100001000000110112000001001001000110001000001000011001001101011000001202000000211
WI-6536          5.7    F      000100010100100000000001110111010000001001000110001000001000011001001111011000021102000000211
WI-961           2.4    F      000020010100100000000001110111010000001001010110001000001000011001001111011000011102000000210
WI-5833          2.4    F      000000010100100000000001110111010000001001012110001000001000011001001111011000011102010000210
WI-6563          5.0    F      000000010100120000000001110111010000001001011110001000001000011001001111011010011202010000210
WI-1172          8.4    F      000000010100100000000001110111010010001001011110001000001100011001001011011010011102010000210
WI-8496          6.7    F      000000010100100000000001110111010010001001011110001000002100011001001010111011001102000000210
    The placement marker is indicated by a 'P' followed by the LOD score relative to the next most likely placement. If it is marked 'P>3' then there we no other placements that were less than LOD 3.0 less likely.
If you have questions or comments, please contact:

humanSTShelp@genome.wi.mit.edu

Last Modified November 4, 1998