an introduction to bioinformatics molecular biology databases

An Introduction to Bioinformatics

Molecular Biology Databases

AIMS

OBJECTIVES

To introduce the major databases- nucleotide- protein

To explain how to search the appropriate databases

To explain how to retrieve information from databases

Choose appropriate databases for information retrieval

Use of Boolean operators to search databases

Retrieve nucleotide and protein sequence files

Introduction

• Hundreds!

• Databases of databases!

• Acronym rich!

• Subcomponents• organisms• structure• metabolism…….

• Searched• text, sequences

Historically

• 1960s •Mary Dayhoff - Protein Sequences

(Eck, R. V., and M. O. Dayhoff. 1966. Atlas of Protein Sequence and Structure 1966.

National Biomedical Research Foundation, Silver Spring, Maryland.)

• 1980s - explosion in DNA sequences• EMBL (European Molecular Biology Laboratory)• NIH (National Institute of Health) Genbank• DDBJ (DNA database of Japan)

• 1988• agreed on international collaboration

• Experimentally determined nucleotide sequence,• Inferred protein sequence

– EMBL, GenBank, DDBJ nucleotides– GenPept– PIR Protein Identification Resource proteins– SWISS-PROT

• Which to choose?

Primary Databases

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Composite Databases

SWISS-PROT + PIR+ GenPept +

SWISS-PROT, Swissnew, Trembl, Tremblnew, Genbank, PIR, Wormpep and PDB

Secondary Databases

• Analytical results of primary databases

• Searching for related patterns

– Prosite– Pfam More on these later

Sub-Databases

• EST - Expressed Sequence Tags

• STS - Sequence Tagged Sites

• SNP - Single Nucleotide Polymorphisms

• OMIM - Online Medelian Inheritance in Man

Searching and Retrieval

• Entrez - National Center for Biotechnology Information

• SRS - European Bioinformatics Institute

• DBGET - Japan’s GenomeNet.

Capable of retrieving specific nucleotide or protein sequence.Provide links to additional related information.

Entrez

Entrez Tutorial

• Search for penicillin-binding genes• Search for Mycobacterium tuberculosis• Combine the searches• Scan the output

Q/ Are there any genes that code for penicillin binding in the Mycobacterium genome?

Example of a text based search to identify genes that have already been annotated.

#1 AND #2

SRS guide

Searching the Databases

• Subject

• Accession Numbers

• Author

e.g. AF208262

Boolean Operators

AND will locate all records containing both the words e.g. human AND protease

OR will locate all records containing either word not necessarily both e.g. human OR protease)

NOT will locate records containing one word, but NOT the other word e.g. human NOT protease