Electronic and Genomic Resources
Chromosome 1 Web Sites
Two web sites (see Table 7 for Internet addresses) specifically dedicated to chromosome 1 have been established and serve as excellent starting points for locating chromosome-specific genomic data,information, and resources. The Chromosome 1 Home Page has been described extensively in a previous Workshop Report (Vance et al., 1997). This site includes sections for chromosome 1 maps and data directly contributed by various researchers, links to other chromosome 1-specific Internet resources, an on-line discussion forum for posting of relevant messages, and information about all Chromosome 1 Workshops, including expanded on-line versions of each Workshop Report. Details regarding the Chromosome 1 email list, which is a listserv that allows email discussion of research topics and dissemination of topical chromosome 1 news, can also be found here. To subscribe to the email group, send an email message to lists@genome.chop.edu with <subscribe Chr1_list > in the body of the message. The email group currently reaches subscribers from 18 countries.
Several new features have been added to the Chromosome 1 Home Page since the last workshop. Most importantly, the web site has been mirrored at the European Bioinformatics Institute, which will be expedient for users residing in European countries. As the Home Page is increasingly utilized by non-scientists, a section that lists informational resources for the general public, including links to resources about chromosomal abnormalities, has been established. Also, a site map and ubiquitous navigation bars have been included for ease of use. Finally, the entire site has been re-designed to provide optimal utility. Suggestions for additions or improvements to this site are welcomed.
The second site is the Human Chromosome 1 Page, which serves as a repository for mapping and sequencing data generated by the Sanger Centre chromosome 1 sequencing project (Table 7). This site utilizes a number of interactive programs to access, view, and retrieve chromosome 1 data. The Sanger Centre data is compiled and stored in a customized, object-oriented database (1ace) that is modeled after acedb (Durbin and Thierry Mieg, 1991). The 1ace application and data files can be downloaded and run externally. In addition, Sanger has created powerful on-line search capabilities of 1ace, with preformatted queries for simple access, the web-based interface "Webace" for more complex queries, and open access using the tace query language for advanced searches.
Mapping tools available at the Sanger site include a graphical display of the Sanger Centre chromosome 1 RH map with clickable links directly to 1ace and query forms and graphical displays of sequence-ready contigs. Sequence files for both finished and unfinished sequence tracts can be readily viewed or downloaded. A recent addition is a BLAST server implementation that specifically searches only within Sanger-generated chromosome 1 data. Additional software and descriptions of projects and protocols are also posted. All of the mapping and sequencing raw data can be obtained from the Sanger Centre ftp site.
Specific genomic resources
Several Internet sites containing relevant and informative chromosome 1 data have been designed since the 1997 workshop report (Table 7). The Bioinformatics Library (BioLib) project has developed a java-based web site that provides interactive, graphical viewing of a number of public genome maps. Genetic, RH, and transcript maps from the NCBI Gene Map project and Unigene collection of transcripts, Stanford Human Genome Center, Généthon, the Whitehead Institute Center for Genome Research, and Online Mendelian Inheritance in Man (OMIM) for chromosome 1 can be viewed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and GENATLAS are database projects designed to catalog genes by their underlying biochemical functions (Kanehisa, 1997). Both databases can be queried by text-based methods or via clickable ideograms that link cytogenetic map positions to transcripts or specific disease genes. GENATLAS also includes a human-mouse comparative map in its catalog. The Genome Database has recently added two helpful features for viewing chromosome 1 mapping information: a listing of chromosome 1 disease genes by cytogenetic position with links to OMIM disorder reports, and a sophisticated interface for viewing whole chromosome and regional maps using the Mapview applet (Fasman et al., 1997). Mapview is an interactive java application that features map customization and marker hypertext links; the related web site allows users to define the map region for viewing by entering flanking markers, cytogenetic bands, or map distance ranges (Letovsky et al., 1998).