[DE] WWW server for The Human Genome Project at Columbia University

"Weider Chang"weider at CUHHCA.HHMI.COLUMBIA.EDU "Weider Chang"weider at CUHHCA.HHMI.COLUMBIA.EDU
Thu Jul 6 15:12:52 EST 1995


[ Article crossposted from bionet.software ]
[ Posted on 9 May 1995 06:19:25 -0700 ]

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.


*************************************************************************
*  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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