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WI/MIT Mouse Radiation Hybrid Mapper
![[LOGO]](/icons/dna.small.gif)
Mouse Radiation Hybrid Mapping
This form allows you to map RH vectors relative to the Whitehead Institute/MIT
Center for Genome Research's radiation hybrid map of the mouse genome.
Enter the radiation hybrid screening results for your marker here. At
regular intervals a software program will assign your marker to
chromosomes and find their best positions on the framework maps. The
results will be mailed back to you, usually within an hour.
Note that this server does not store your RH data or provide
submission to other databases. Before publishing your RH results, it
is important to submit your raw data to one of the two public
databases that curate the complete data set for the T31 RH panel.
Please submit your T31 RH data to either
The Jackson Laboratory Mouse
Radiation Hybrid Database
or to
RHdb at the European Bioinformatics Institute
Please see the instructions before proceeding,
including details about the LOD scores displayed with the results.
To use this service, follow these instructions carefully.
- Screen your markers by PCR on the T31 Radiation Hybrid
screening panel. This panel is available through
Research Genetics.
- Format the screening results as a vector of 0's and 1's in T31 hybrid numerical order.
Unknown/uncertain data should be indicated
with dashes (-) or 2's. You may use spaces to improve
readability, but this isn't necessary
- Arrange the results in a table: STS name first and then the
data vector. Here is an example (not all 100 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
- 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.
- 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).
- 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!
- 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.
- 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.
- 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.
- 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.
Suggest or Complain to:
Huy Nguyen
Last modified: Wed Dec 15 12:03:37 EST 1999