Announcement: WWW server for The Human Genome Project at Columbia University
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URL http://genome1.ccc.columbia.edu/~genome/
This Chromosome 13 WWW server contains information on maps, databases and
software produced by the project.
1. Our methodology:
Our approach involves hybridization of the inter-Alu PCR products of CEPH
YACs to a chromosome 13 cosmid library. All cosmids identified in a YAC bin
are hybridized to each other to establish cosmid contigs. From the sequence
at one end of a subset of these cosmids, we generate STSs. Finally, assorted
genes, cDNAs and other markers have been hybridized or PCR'd to CH13 YACs,
and occasionally to cosmids. The following hybridization data are stored in
our database:
YAC<=>cosmid
(YACs and cosmids are named according to their positions in the CEPH and
Los Alamos library arrays.)
cosmid<=>cosmid
STS<=>YAC
(By definition, the STS name is the CH13 cosmid from which it
was derived. Thus, this also provides information on cosmid<=>YAC
relationships.)
Marker<=>YAC
(Marker names are highly variable, and depend on the naming
conventions established by GDB or individual investigators.)
A search engine has been written in perl, that interact with the Sybase
databases, is available for querying these relationships through
the server.
2. Raw data.
The raw hybridization data files, which are generated from the Sybase
database, are also available through the WWW server.
YAC to Cosmids hybridization file
STS to YACS hybridization file
Cosmid to Cosmids hybridization file
Marker to Cosmids hybridization file
3. Maps
Two types of maps are available. They are YAC maps of Yacs with shared
cosmids, and YAC maps that include cosmid hybridization matrix.
These maps can be called up by selecting the proper hyper-link for YACs
that have such maps. The detail information on how to read these
maps is also available.
4. Primer Sequences
The primer sequences on STSs that are generated by our group is also
available through the WWW server. PCR conditions are standard, and an
annealing temperature of 60 C is adequate for amplification of all the STSs.
All STSs have been submitted to GDB, and D numbers and accession numbers
are included with the sequences. Further information is available by
consulting GDB
5. Our Future Goals
In upcoming installments, we will provide an unified map covering the length
of the q arm of chromosome 13. The map, as well as the above lists and
tables, will be continuously updated as additional information is obtained.
Eventually, we expect to have a clickable, expandable map of CH13 summarizing
most of the available data from Columbia and other sources. Mapping software
developed by our Informatics program will also be available to anyone
interested through this page.
Please send your comments and bug reports to genome at genome1.ccc.columbia.edu.
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* Weider Chang, Ph.D *
* Department of Biochemistry & Molecular Biophysics *
* Columbia University *
* 630 W 168th St. NY, NY 10032 *
* *
* Email: weider at cuhhca.hhmi.columbia.edu Tel: (212)305-4270 *
* weider at genome1.ccc.columbia.edu Fax: (212)305-7379 *
* weider at cs.columbia.edu *
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