- Email: [email protected]
Web alert
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Genetics of disease Web alert Tyra G Wolfsberg*, Izabela Makalowska† and Wojciech Makalowski‡ A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Genetics & Development. Addresses *National Human Genome Research Institute, National Institutes of Health, Building 9, Room B1E01, Bethesda, Maryland 20892-0960, USA; e-mail: [email protected] †National Human Genome Research Institute, National Institutes of Health, Building 49, Room 2B75, Bethesda, Maryland 20892-4431, USA; e-mail: [email protected] ‡National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 8N-805, Bethesda, Maryland 20894, USA; e-mail: [email protected] Current Opinion in Genetics & Development 2001, 11:237–238.
Genome and genetic databases NCBI’s Map Viewer http://www.ncbi.nlm.nih.gov/cgibin/Entrez/hum_srch?chr=hum_chr.inf&query UCSC’s Genome Browser http://genome.ucsc.edu/ Ensembl http://www.ensembl.org/ All three sites provide views and analyses of the publicly available draft human genome sequence. Both NCBI and UCSC are assembling the pieces of draft nucleotide sequence into longer contigs, and Ensembl — a joint project between EMBL–EBI and the Sanger Centre — is currently displaying the UCSC assembly. All three projects provide text and sequence-based entries into the genome, as well as a graphical interface to the sequence. The three sites are in the process of annotating features, including genes and proteins, as well as aligning known sequences, like ESTs and mRNAs, on the genome. NCBI integrates extensive sequence, cytogenetic, genetic, and radiation hybrid maps, whereas UCSC and Ensembl display many novel protein predictions.
about the disease, sequence, genetic, and literature databases, as well as patient information sites. Online Mendelian Inheritance in Man (OMIM) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM OMIM is a catalog of human genes and genetic disorders authored and edited by Victor McKusick and his colleagues. Queries to OMIM are now even more powerful, as it has recently been integrated into the NCBI’s ‘Entrez’ system. OMIM contains textual information, pictures, and reference information, as well as links to MEDLINE articles and sequence information already in Entrez. Gene Cards Project http://bioinformatics.weizmann.ac.il/cards/ ‘GeneCards’ is a dictionary-like database that integrates biomedical knowledge from several sources and presents it as an overview. An individual GeneCard gives the information about important features of a gene: the official name, a list of synonyms, homologous genes in the mouse, the locus of the gene and of its homologs, the name of its product(s), the main features of this/these product(s), a list of disorders in which the gene is involved, and medical applications, like new therapies and diagnoses. Human Gene Mutation Database http://www.uwcm.ac.uk/uwcm/mg/hgmd0.html The ‘Human Gene Mutation Database’ is a repository of gene lesions responsible for human inherited disease. It currently lists >20,000 mutations in 1000 genes. It includes only human nuclear genes, and most of them show a phenotype. It now also includes disease-associated sequence polymorphisms. International Human Genome Sequencing Consortium Genome Hub http://www.nhgri.nih.gov/genome_hub.html The ‘Genome Hub’ lists links to sites that provide genomic and other sequence information. Most sites in the list have a human focus but web pages for other organisms are included as well.
Ensembl Trace Server http://trace.ensembl.org/
Genetics and health NCBI Trace Archive http://www.ncbi.nlm.nih.gov/Traces/ The two trace repositories, which exchange data regularly, provide a permanent archive for single pass (i.e. unverified) DNA sequencing reads and associated traces and quality values. These data come from whole-genome shotgun projects, EST projects, and other large-scale sequencing projects. Much of the mouse genomic data from the public sequencing efforts is now in these repositories, and can be found by BLAST searches. Genes and Disease http://www.ncbi.nlm.nih.gov/disease/ This site, sponsored by the NCBI, provides information about many mapped human disease genes. It includes information
Rare Genetic Diseases In Children: The Rare Disease Catalogue http://mcrcr2.med.nyu.edu/murphp01/disease.htm This ‘Disease Catalog’ provides a comprehensive list of web sites dedicated to specific genetic diseases. Diseases are listed alphabetically, and each entry is linked to the appropriate OMIM citation, as well as to organizations that can provide additional information. WHO Human Genetics Programme http://www.who.int/ncd/hgn/ The ‘Human Genetics Programme’ is an arm of the World Health Organization that develops genetic approaches to prevent and control common hereditary diseases.
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Web alert
ClinicalTrials.gov http://www.clinicaltrials.gov/ This site at the National Insitutes of Health provides information on >5000 clinical studies sponsored by the NIH and other US Federal agencies. Studies from the pharmaceutical industry will be added soon.
Microarrays GenomeWeb http://dns.cbi.pku.edu.cn/GenomeWeb/ ‘GenomeWeb’, a product of the UK Human Genome Mapping Project Resource Center, provides up-to-date, verified links to
many genome-related resources. For example, the ‘Gene Expression and Microarray’ page provides a collection of links that describe microarry protocols, database tools, mining tools, public databases and commercial database tools. DNA Microarray (Genome Chip) — Monitoring the Genome on a Chip http://www.gene-chips.com/ This page, maintained by Leming Shi, provides information on DNA microarray technology as well as list of related academic and industrial links. It contains information about the basic concept, design, applications, data mining, software, meetings, lists of articles related to this technology, and more.
Genetics of disease Web alert Tyra G Wolfsberg*, Izabela Makalowska† and Wojciech Makalowski‡ A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Genetics & Development. Addresses *National Human Genome Research Institute, National Institutes of Health, Building 9, Room B1E01, Bethesda, Maryland 20892-0960, USA; e-mail: [email protected] †National Human Genome Research Institute, National Institutes of Health, Building 49, Room 2B75, Bethesda, Maryland 20892-4431, USA; e-mail: [email protected] ‡National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 8N-805, Bethesda, Maryland 20894, USA; e-mail: [email protected] Current Opinion in Genetics & Development 2001, 11:237–238.
Genome and genetic databases NCBI’s Map Viewer http://www.ncbi.nlm.nih.gov/cgibin/Entrez/hum_srch?chr=hum_chr.inf&query UCSC’s Genome Browser http://genome.ucsc.edu/ Ensembl http://www.ensembl.org/ All three sites provide views and analyses of the publicly available draft human genome sequence. Both NCBI and UCSC are assembling the pieces of draft nucleotide sequence into longer contigs, and Ensembl — a joint project between EMBL–EBI and the Sanger Centre — is currently displaying the UCSC assembly. All three projects provide text and sequence-based entries into the genome, as well as a graphical interface to the sequence. The three sites are in the process of annotating features, including genes and proteins, as well as aligning known sequences, like ESTs and mRNAs, on the genome. NCBI integrates extensive sequence, cytogenetic, genetic, and radiation hybrid maps, whereas UCSC and Ensembl display many novel protein predictions.
about the disease, sequence, genetic, and literature databases, as well as patient information sites. Online Mendelian Inheritance in Man (OMIM) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM OMIM is a catalog of human genes and genetic disorders authored and edited by Victor McKusick and his colleagues. Queries to OMIM are now even more powerful, as it has recently been integrated into the NCBI’s ‘Entrez’ system. OMIM contains textual information, pictures, and reference information, as well as links to MEDLINE articles and sequence information already in Entrez. Gene Cards Project http://bioinformatics.weizmann.ac.il/cards/ ‘GeneCards’ is a dictionary-like database that integrates biomedical knowledge from several sources and presents it as an overview. An individual GeneCard gives the information about important features of a gene: the official name, a list of synonyms, homologous genes in the mouse, the locus of the gene and of its homologs, the name of its product(s), the main features of this/these product(s), a list of disorders in which the gene is involved, and medical applications, like new therapies and diagnoses. Human Gene Mutation Database http://www.uwcm.ac.uk/uwcm/mg/hgmd0.html The ‘Human Gene Mutation Database’ is a repository of gene lesions responsible for human inherited disease. It currently lists >20,000 mutations in 1000 genes. It includes only human nuclear genes, and most of them show a phenotype. It now also includes disease-associated sequence polymorphisms. International Human Genome Sequencing Consortium Genome Hub http://www.nhgri.nih.gov/genome_hub.html The ‘Genome Hub’ lists links to sites that provide genomic and other sequence information. Most sites in the list have a human focus but web pages for other organisms are included as well.
Ensembl Trace Server http://trace.ensembl.org/
Genetics and health NCBI Trace Archive http://www.ncbi.nlm.nih.gov/Traces/ The two trace repositories, which exchange data regularly, provide a permanent archive for single pass (i.e. unverified) DNA sequencing reads and associated traces and quality values. These data come from whole-genome shotgun projects, EST projects, and other large-scale sequencing projects. Much of the mouse genomic data from the public sequencing efforts is now in these repositories, and can be found by BLAST searches. Genes and Disease http://www.ncbi.nlm.nih.gov/disease/ This site, sponsored by the NCBI, provides information about many mapped human disease genes. It includes information
Rare Genetic Diseases In Children: The Rare Disease Catalogue http://mcrcr2.med.nyu.edu/murphp01/disease.htm This ‘Disease Catalog’ provides a comprehensive list of web sites dedicated to specific genetic diseases. Diseases are listed alphabetically, and each entry is linked to the appropriate OMIM citation, as well as to organizations that can provide additional information. WHO Human Genetics Programme http://www.who.int/ncd/hgn/ The ‘Human Genetics Programme’ is an arm of the World Health Organization that develops genetic approaches to prevent and control common hereditary diseases.
238
Web alert
ClinicalTrials.gov http://www.clinicaltrials.gov/ This site at the National Insitutes of Health provides information on >5000 clinical studies sponsored by the NIH and other US Federal agencies. Studies from the pharmaceutical industry will be added soon.
Microarrays GenomeWeb http://dns.cbi.pku.edu.cn/GenomeWeb/ ‘GenomeWeb’, a product of the UK Human Genome Mapping Project Resource Center, provides up-to-date, verified links to
many genome-related resources. For example, the ‘Gene Expression and Microarray’ page provides a collection of links that describe microarry protocols, database tools, mining tools, public databases and commercial database tools. DNA Microarray (Genome Chip) — Monitoring the Genome on a Chip http://www.gene-chips.com/ This page, maintained by Leming Shi, provides information on DNA microarray technology as well as list of related academic and industrial links. It contains information about the basic concept, design, applications, data mining, software, meetings, lists of articles related to this technology, and more.