What is bioinformatics?

Definition

Bioinformatics is the use of mathematics, informatics, computer science, statistics, and chemistry to solve biological problems. These problems are often on the molecular or evolutionary level, often overlapping with systems biology. Examples of common bioinformatics tasks include sequence or structure alignment, genome assembly, [[protein structure prediction]], gene expression predictions, evolutionary modeling, and protein-protein interactions. A common paradigm in bioinformatics is the use of mathematical algorithms to extract useful information from data obtained from high throughput methods such as genome sequencing, DNA microarrays or protein information from [[mass spectrometry]].

Applications

We will now look at several of the applications mentioned above.

Protein structure prediction

While the primary structure of a protein (ie, amino acid sequence) can be easily determined from the DNA sequence, secondary, tertiary, and quaternary structures require NMR or crystallography. Bioinformatics can also be used to predict these higher-level protein structures or enhance information obtained from NMR or crystallography. [[Protein homology modeling]] is often employed to predict structures of related proteins, when the structure of a homologous protein is known.

Comparative genomics

Comparative genomics refers to the correspondence of genomic features in different organisms. The construction of intergenomic maps can allow the tracing of evolutionary processes that lead to the divergence of different genomes. Information can range from point mutations all the way up to the duplication of large chromosomal segments.

Sequence analysis

Sequence analysis refers to the determination of genes that encode peptides or regulatory sequences using sequence information. Software and powerful computers are used to analyze the genome of thousands of organisms, compensating for DNA mutations, and identifying sequences that are related. Sequence analysis is also used in shotgun sequencing techniques. In shotgun sequencing, the sequence of thousands of DNA fragments (600-800 bp) are determined and software is used to detect fragment overlap and assemble the complete genome.

Genome annotation

Genome annotation refers to the marking of genomes to indicate protein coding and regulatory sequences. This has become a very important part of the natural successor to the Human Genome Project, the Human Proteome Project.

Computational evolutionary biology

Computational evolutionary biology has allowed researchers to trace the evolution of organisms by looking at changes in their DNA. Entire genomes can now be compared, allowing the study of complex evolutionary events such as [[gene duplication]] and lateral gene transfer.

Gene expression analysis

Gene expression can be determined by measuring mRNA levels with techniques such as microarrays, [[expressed sequence tags]] (ESTs), serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS), or in situ hybridization. Statistical tools have been developed to separate signal from noise in these high throughput data. Algorithms can be used along with experimental data to determine genes that are upregulated or downregulated in a particular disease.

Protein expression analysis

Analagous to gene expression analysis, protein microarrays and mass spectrometry can provide an overview of the proteins present in a sample. Bioinformatics is very important in interpreting the large amount of data provided by these techniques.

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Featured Bioinformatics Book

Probabilistic Modelling in Bioinformatics and Medical Informatics

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