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Detailed overview of biological sequence retrieval.

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by

Usman Mirza

on 10 January 2015

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Transcript of Detailed overview of biological sequence retrieval.

Part 1: Detailed overview of biological sequence retrieval.

Biological databases
What is a database and what are the features of an ideal db?

What are the relationships/differences between primary and derived sequence databases?

Significance of Biological databases?


A brief history of biological databases
1965: M. O. Dayhoff et al. publish “Atlas of Protein Sequences and Structures”
1982: EMBL initiates DNA sequence database, followed within a year by GenBank (then at LANL) and in 1984 by DNA Database of Japan
1988: EMBL/GenBank/DDBJ agree on common format for data elements

The National Center for Biotechnology Information
Establish public databases
Research in computational biology
Develop software tools for sequence analysis
Disseminate biomedical information
NCBI Architechture
What is a database?
Structured collection of information.

Consists of basic units called records or entries.

Each record consists of fields, which hold pre-defined data related to the record.

For example, a protein database would have protein entries as records and protein properties as fields (e.g., name of protein, length, amino-acid sequence)

The NCBI houses a series of databases relevant to biotechnology and biomedicine.

Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for the biomedical literature.

All these databases are available online through the Entrez search engine.
THE ‘PERFECT’ DATABASE
Comprehensive, but easy to search.
Annotated, but not “too annotated”.
A simple, easy to understand structure.
Cross-referenced.
Minimum redundancy.
Easy retrieval of data.

Review questions?
1. What type of information is there in the complex, highly compact multistep process of central dogma?
2. How we can use this information?
3. How alternative splicing give rise to a large number of transcripts?
Central Dogma
Thank you
Any question?
Full transcript