Bioinformatics

Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as a specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics.

Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes.

As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret biological data.

The components of information engineering include more theoretical fields such as machine learning, artificial intelligence, control theory, signal processing, and information theory, and more applied fields such as computer vision, natural language processing, bioinformatics, medical image computing, cheminformatics, autonomous robotics, mobile robotics, and telecommunications.

A pioneer in the field was Margaret Oakley Dayhoff.

Margaret Belle (Oakley) Dayhoff (March 11, 1925 – February 5, 1983) was an American physical chemist and a pioneer in the field of bioinformatics.

In experimental molecular biology, bioinformatics techniques such as image and signal processing allow extraction of useful results from large amounts of raw data.

Much of molecular biology is quantitative, and recently much work has been done at its interface with computer science in bioinformatics and computational biology.

Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein–protein interactions, genome-wide association studies, the modeling of evolution and cell division/mitosis.

In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences.

Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein–protein interactions, genome-wide association studies, the modeling of evolution and cell division/mitosis.

In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence.

Examples include: pattern recognition, data mining, machine learning algorithms, and visualization.

Biology data visualization is a branch of bioinformatics concerned with the application of computer graphics, scientific visualization, and information visualization to different areas of the life sciences.

Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein–protein interactions, genome-wide association studies, the modeling of evolution and cell division/mitosis.

Protein structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry; it is highly important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes).

Paulien Hogeweg and Ben Hesper coined it in 1970 to refer to the study of information processes in biotic systems.

In 1970, together with Ben Hesper, she defined the term bioinformatics as "the study of informatic processes in biotic systems".

Biological computation uses bioengineering and biology to build biological computers, whereas bioinformatics uses computation to better understand biology.

Biological engineering employs knowledge and expertise from a number of pure and applied sciences, such as mass and heat transfer, kinetics, biocatalysts, biomechanics, bioinformatics, separation and purification processes, bioreactor design, surface science, fluid mechanics, thermodynamics, and polymer science.

At a more integrative level, it helps analyze and catalogue the biological pathways and networks that are an important part of systems biology.

Indeed, the focus on the dynamics of the studied systems is the main conceptual difference between systems biology and bioinformatics.

One can then apply clustering algorithms to that expression data to determine which genes are co-expressed.

It is a main task of exploratory data mining, and a common technique for statistical data analysis, used in many fields, including machine learning, pattern recognition, image analysis, information retrieval, bioinformatics, data compression, and computer graphics.

Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein–protein interactions, genome-wide association studies, the modeling of evolution and cell division/mitosis.

Predicting the function of a gene and confirming that the gene prediction is accurate still demands in vivo experimentation through gene knockout and other assays, although frontiers of bioinformatics research are making it increasingly possible to predict the function of a gene based on its sequence alone.

Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein–protein interactions, genome-wide association studies, the modeling of evolution and cell division/mitosis.

It is also directly associated with bioinformatics, computational biology and Artificial life.

Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data.

Examples include quantum information processing, an amalgamation of quantum physics and computer science, and bioinformatics, combining molecular biology with computer science.

Today, computer programs such as BLAST are used daily to search sequences from more than 260 000 organisms, containing over 190 billion nucleotides.

In bioinformatics, BLAST (basic local alignment search tool) is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences.

For the special task of taxonomic classification of sequence snippets, modern k-mer based software like Kraken achieves throughput unreachable by alignment methods.

In bioinformatics, k-mers are subsequences of length k contained within a biological sequence.

The actual process of analyzing and interpreting data is referred to as computational biology.

Computational biology is different from biological computing, which is a subfield of computer science and computer engineering using bioengineering and biology to build computers, but is similar to bioinformatics, which is an interdisciplinary science using computers to store and process biological data.

The algorithms in turn depend on theoretical foundations such as discrete mathematics, control theory, system theory, information theory, and statistics.

The theory has also found applications in other areas, including statistical inference, natural language processing, cryptography, neurobiology, human vision, the evolution and function of molecular codes (bioinformatics), model selection in statistics, thermal physics, quantum computing, linguistics, plagiarism detection, pattern recognition, and anomaly detection.

Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein–protein interactions, genome-wide association studies, the modeling of evolution and cell division/mitosis.

Structural alignments are especially useful in analyzing data from structural genomics and proteomics efforts, and they can be used as comparison points to evaluate alignments produced by purely sequence-based bioinformatics methods.

It plays a role in the text mining of biological literature and the development of biological and gene ontologies to organize and query biological data.

Scientific researchers incorporate text mining approaches into efforts to organize large sets of text data (i.e., addressing the problem of unstructured data), to determine ideas communicated through text (e.g., sentiment analysis in social media ) and to support scientific discovery in fields such as the life sciences and bioinformatics.

Owen White designed and built a software system to identify the genes encoding all proteins, transfer RNAs, ribosomal RNAs (and other sites) and to make initial functional assignments.

Owen White is a bioinformatician and director of the Institute For Genome Sciences at the University of Maryland School of Medicine.

In structural biology, it aids in the simulation and modeling of DNA, RNA, proteins as well as biomolecular interactions.

A third approach that structural biologists take to understanding structure is bioinformatics to look for patterns among the diverse sequences that give rise to particular shapes.

A comparison of genes within a species or between different species can show similarities between protein functions, or relations between species (the use of molecular systematics to construct phylogenetic trees).

Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetics.

For a genome as large as the human genome, it may take many days of CPU time on large-memory, multiprocessor computers to assemble the fragments, and the resulting assembly usually contains numerous gaps that must be filled in later.

Most (though probably not all) genes have been identified by a combination of high throughput experimental and bioinformatics approaches, yet much work still needs to be done to further elucidate the biological functions of their protein and RNA products.