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