Transcript Databases
Databases July 2002 - CS Course Module: Introduction to Bioinformatics – CS 2001 Types of Database Sequence and Bibliographic Genomic Clinical and Mutation Homologies Integrated Most databases • are accessible from a web page • are interlinked July 2002 - CS Course Module: Introduction to Bioinformatics – CS 2001 Sequence Databases Main nucleic acid sequence databases • EMBL • GenBank • DDBJ Main protein sequence databases • Swiss Prot • also TREMBL, GenPept Often integrated with other databases July 2002 - CS Course Module: Introduction to Bioinformatics – CS 2001 Integrating Sequence and Bibliographic Databases Entrez • Links nucleic acid sequences, protein sequences and MEDLINE • Powerful and easy to use SRS • Universal system for searching sequence and other databases • Available worldwide including at HGMP July 2002 - CS Course Module: Introduction to Bioinformatics – CS 2001 Genomic Databases GDB • Repository for mapping and genomic data for the Human Genome Project • Powerful; links to other databases ACeDB • Developed to provide access to C.elegans data July 2002 - CS Course Module: Introduction to Bioinformatics – CS 2001 Clinical and Mutation Databases OMIM • Online Mendelian Inheritance in Man • Database of disease-linked genes and associated phenotypes • Links to Entrez, GDB and other databases HGMD • Database of sequences and phenotypes of disease-causing mutations Disease-specific mutation databases July 2002 - CS Course Module: Introduction to Bioinformatics – CS 2001 Homology Databases MGI • Mapping and gene expression data for the mouse • Human homologies • Links to GDB and Entrez Many other organism-specific databases • can be used to search for homologs of human genes July 2002 - CS Course Module: Introduction to Bioinformatics – CS 2001 An Integrated Database GeneCards • Integrated resource of information on human genes and their products • Major emphasis on human disease • Links to many kinds of biomedical information • Sequence databases • OMIM, HGMD, MDB • Doctors’ Guide to the Internet July 2002 - CS Course Module: Introduction to Bioinformatics – CS 2001 Database Searching Tips Look for links to Help or Examples Try Boolean searches Be careful with UK/US spelling differences leukaemia vs leukemia haemoglobin vs hemoglobin colour vs color July 2002 - CS Course Module: Introduction to Bioinformatics – CS 2001