Chromosome 1 Websites

Three directories specific for chromosome 1 data, information, and resources are now available on the Internet, each of which are excellent starting points for finding on-line information available for chromosome 1 (see Table 1 for Internet addresses mentioned in this section). The Chromosome 1 Home Page, originally established in 1995 to serve the Second Chromosome 1 Workshop, currently has its primary node at Rutgers University and a European mirror at the European Bioinformatics Institute (EBI) (Matise et al., this report). The site has now expanded to include a wide array of services, including all previous and future Workshop reports and information, a repository for and link to chromosome 1-specific data, an on-line discussion forum for chromosome 1 research topics, a directory of researchers working on chromosome 1-specific projects, and a section of information and resources useful for the general public. Chromosome 1 researchers can discuss and receive current information and updates by subscribing to the Chromosome 1 email list. Subscription to the list is accomplished by sending an Email message to lists@genome.chop.edu with the word "subscribe Chr1_list" in the body of the message.

Most of the Chromosome 1 Home Page content and features have been described in previous workshop reports (Gregory et al., 1998; Vance et al., 1997), but several items have been recently added. A research directory service lists the name, contact information, and research interests of chromosome 1 investigators, and this service also allows additional researchers to automatically add their names to the directory (currently listing 31 research groups). A large number of new chromosome 1 data and informational resources have been added to the resources section, which has been divided into nine categories: genetic maps, radiation hybrid maps, cytogenetic maps, transcript maps, sequence, integrated maps, comparative maps, genomic databases, and genomic resources. The resources section now includes over 100 chromosome 1-specific Internet links. Server statistics for the entire site are now also available, and the site was accessed approximately 35,000 times in the last year.

The Human Genome Organization (HUGO) has generated chromosome-specific resource pages for each human chromosome, including chromosome 1, and these pages are updated by the HUGO Single Chromosome Committees (Table 1). The organization and content of the HUGO chromosome 1 page is very similar to the Chromosome 1 Home Page resources section, providing Internet links to chromosome 1-specific data, DNA sequencing and annotation information, disease-specific loci sites, model organism synteny maps, and medical information for parents and health professionals.

The Sanger Centre's Human Chromosome 1 Page (Table 1) serves as a repository for data generated by Sanger's chromosome 1 mapping and sequencing teams (see Sanger Centre section). This site has been introduced in previous Workshop reports, but new features have emerged since the last workshop (Gregory et al., 1998; Vance et al., 1997). The site is now organized into several sections: an overview page which includes links to primary sequence data, a mapping section detailing radiation hybrid (RH) and large-insert clone mapping efforts, sequence progress statistics, and chromosome 1- and Sanger-specific BLAST utilities. Sanger's data is stored and organized using the object-oriented database 1ace, modeled after ACEDB (Durbin and Thierry Mieg, 1991). Users can directly download map and sequence data files for viewing externally, or they can use a number of web tools for data viewing and analysis provided from the Sanger website. The entire Sanger mapping and sequencing data set has recently been indexed for both simple and complex (using AltaVista) text searching using keywords such as marker/gene name, large-insert clone ID, or DNA sequence (AceBrowser). The 1ace database can also be more precisely searched on-line using the Webace interface, either at the sequence or sequence feature level. Open search access to 1ace is provided for users familiar with ACEDB commands. Primary sequence and mapping data is displayed with a choice of plain text, hypertext, static graphic or dynamic graphical viewing. Webace also creates graphics of sequenced and annotated clones and clone contigs which display known and predicted sequence features such as open reading frames, characterized genes, repetitive elements, and polymorphisms. While many sequence features are incorporated into the EMBL/GenBank-submitted records, a great deal more information about each clone and sequence is available at the Sanger site, and the details are presented in a much richer fashion. Additional software and descriptions of projects and protocols are also available at the Sanger chromosome 1 site, and all of the mapping and sequencing raw data can be obtained from the Sanger Centre ftp site.

Internet Resources

Several Internet sites containing relevant and informative chromosome 1 data have been developed since the last workshop report (Table 1). The most comprehensive of these is CompView, a chromosome 1-specific project that combines polymorphic, RH, cytogenetic, large-insert clone, and transcript mapping information together into a single, integrated map and searchable/viewable database (see Computational Maps) (White et al., 1999). The newly redesigned National Center for Biotechnology Information (NCBI) Website has a large amount of genomic information that can be extracted for chromosome 1. This includes the updated GeneMap '99 transcript map (Deloukas et al., 1998), expressed sequence tag (EST) clusters for chromosome 1 using UniGene (Boguski and Schuler, 1995), the KARIBIN resource which assigns cytogenetic positions to a variety of polymorphic markers and large-insert clones (Zhang et al., 1999), and a chromosomal aberrations map maintained by the National Cancer Institute's Cancer Chromosome Aberration Project. Another site containing abundant chromosome-specific information is at the Oak Ridge National Laboratories (ORNL). The ORNL site contains a genome catalog displaying chromosome 1 sequence and mapping information generated from the Human Genome Project, providing an overview of structural and functional features of mapped and sequenced large-insert clones. Clone sequences can also be graphically viewed for content using ONRL's Genome Channel utility (Mural et al., 1999). These and other resources provided by ORNL are conveniently listed and summarized for chromosome 1 at the site's Human Chromosome Launchpad.

Because of the rapid generation of chromosome 1 sequence data, both the EBI and the NCBI have designed tools for monitoring the latest sequence progress (Table 1). The EBI Genome Monitoring Table lists real time statistics for the total amount of finished and draft sequence for each human chromosome (Beck and Sterk, 1998). The NCBI site lists all sequence contigs for each chromosome, sorted either by chromosomal position or sequence size (Jang et al., 1999). As of this writing, there were 130 contigs representing 22.1 Mb of finished chromosome 1 sequence.

A number of new, specialized databases also provide data sorted by chromosome. SERGG, the SouthEastern Regional Genetics Group, provides a searchable database interface for a large number of archived chromosomal abnormalities, which currently includes over 50 chromosome 1 entries. A related database, the Atlas of Genetics and Cytogenetics in Oncology and Haematology at INFOBIOGEN, lists characterized cytogenetic clinical and gene-specific abnormalities for chromosome 1 (Dorkeld et al., 1999). Finally, the Coriell Cell Repositories now displays their considerable collection of chromosomal resources in graphic format, organized into groups as somatic cell hybrids, translocations, and copy number abnormalities.