Bioinformatics Crash Course For Everyone

Broad Coverage of Bioinformatics

Bioinformatics covers many specialized and advanced areas of biology.

Functional genomics:

Identification of genes and their respective functions.

Structural genomics:

Predictions related to functions of proteins.

Comparative genomics:

For understanding the genomes of different species of organisms.

DNA microarrays:

These are designed to measure the levels of gene expression in different tissues, various stages of development and in different diseases.

Medical informatics:

This involves the management of biomedical data with special referee to biomolecules, in vitro assays and clinical trials.

Components of Bioinformatics

Bioinformatics comprises three components:

   1. Creation of databases

   2. Development of algorithms and statistics

   3. Analysis of data and interpretation

Applications of Bioinformatics

A selected list of applications of bioinformatics is given below:

    i. Sequence mapping of biomolecules (DNA, RNA, proteins).

    ii. Identification of nucleotide sequences of functional genes.

    iii. Finding of sites that can be cut by restriction enzymes.

    iv. Designing of primer sequence for polymerase chain reaction.

Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures.

Importance of Biological Database

Databases are important tools in assisting scientists to analyze and explain a host of biological phenomena from the structure of biomolecules and their interaction, to the whole metabolism of organisms and to understanding the evolution of species. This knowledge helps facilitate the fight against diseases, assists in the development of medications, predicting certain genetic diseases and in discovering basic relationships among species in the history of life.

Biological database design, development, and long-term management is a core area of the discipline of bioinformatics

Types of biological database:

There are three to four main types of biological databases on the base of data it contain;

• Primary database

• Secondary Databases

• Specialized Database

• Literature Databases

Entrez is a data retrieval system developed by the National Center for Biotechnology Information (NCBI) that provides integrated access to a wide range of data domains, including literature, nucleotide and protein sequences, complete genomes, three-dimensional structures, and more. Entrez includes powerful search features that retrieve not only the exact search results but also related records within a data domain that might not be retrieved otherwise and associated records across data domains.

FASTA Sequence

FASTA format or sequence is a text-based format for representing either nucleotide sequences or peptide sequences

• a unique identification number (the accession number)

• the version number of the sequence

• the length of the sequence

• molecule type (DNA or mRNA)

• taxonomic division (for instance, INV = invertebrate)

• last release date

• source organism

  
  

Reference Sequence (RefSeq)

The Reference Sequence (RefSeq) collection provides a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.

• Always start with NT for DNA, NM for mRNA, or NP for protein

BLAST

BLAST is a computer algorithm that is available for use online at the National Center for Biotechnology Information (NCBI) website, as well as many other sites. BLAST can rapidly align and compare a query DNA sequence with a database of sequences, which makes it a critical tool in ongoing genomic research.

ClustalW2

ClustalW2 is a general purpose global multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.