Bioinformatics
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BIOINFORMATICS. Ayesha Masrur Khan Spring 2013. Bioinformatics A complete understanding of the term. The National Centre for Biotechnology Information (NCBI 2001) defines bioinformatics as:

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BIOINFORMATICS

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Bioinformatics

BIOINFORMATICS

Ayesha MasrurKhan

Spring 2013

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Bioinformatics a complete understanding of the term

BioinformaticsA complete understanding of the term

The National Centre for Biotechnology Information (NCBI 2001) defines bioinformatics as:

"Bioinformatics is the field of science in which biology, computer science, and information technology merge into a single discipline. There are three important sub-disciplines within bioinformatics: the development of new algorithms and statistics with which to assess relationships among members of large data sets; the analysis and interpretation of various types of data including nucleotide and amino acid sequences, protein domains, and protein structures; and the development and implementation of tools that enable efficient access and management of different types of information."

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Bioinformatics aim

Bioinformatics-Aim

  • It is not just “informatics”

  • Bioinformatics is the field of science in which biology, computer science, mathematics and information technology merge into a single discipline. The ultimate goal of the field is to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in biology can be discerned.

  • We want to be able to understand the words in a sequence sentence that form a particular protein structure, and one day to be able to write sentences (design proteins) of our own.

  • Furthermore, this new knowledge could have profound impacts on fields as varied as human health, agriculture, the environment, energy and biotechnology.

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Bioinformaticists bioinformaticians bioinformatics scientists

Bioinformaticists, Bioinformaticians &Bioinformatics scientists

  • A Bioinformaticist versus a Bioinformatician (1999):

  • Bioinformatics has become a mainstay of genomics, proteomics, and all other *omics (such as phenomics) that many information technology companies have entered the business or are considering entering the business, creating an IT (information technology) and BT (biotechnology) convergence.

  • A bioinformaticist is an expert who not only knows how to use bioinformatics tools, but also knows how to write interfaces for effective use of the tools.

  • A bioinformatician, on the other hand, is a trained individual who only knows how to use bioinformatics tools without a deeper understanding.

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Bioinformaticists bioinformaticians bioinformatics scientists1

Bioinformaticists, Bioinformaticians &Bioinformatics scientists

  • There are bioinformaticists interested in the theory behind the manipulation of that data and there are bioinformatics scientists concerned with the data itself and its biological implications.

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Challenges facing the bioinformatics community

Challenges facing the bioinformatics community

Mass of Data

-Need to provide easy and reliable access to this data

  • This data itself is meaningless before analysis and the sheer volume present makes it impossible for even a trained biologist to begin to interpret it manually

  • Incisive computer tools must be developed to allow the extraction of meaningful biological information

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Bioinformatics

Earliest Efforts in Bioinformatics

  • Bioinformatics started over a century ago by Gregor Mendel, known as Father of Genetics Genetic record keeping

  • He cross-fertilized different colors of the same species of flowers and kept careful records of the colors of flowers that he cross-fertilized and the color(s) of flowers they produced.

  • Mendel illustrated that the inheritance of traits could be more easily explained if it was controlled by factors passed down from generation to generation.

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Bioinformatics

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Bioinformatics

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Bioinformatics

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Terms that need to be understood

Terms that need to be understood

  • Homology-denotes an absolute divergent relationship between sequences.

  • Analogy-can denote, based on similar folds or catalytic residues similarity, either divergent or convergent relationship.

  • Orthology-Proteins that perform same functions in different species.

  • Paralogy-Proteins that perform different but related functions within on organism.

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Origin of bioinformatic biological databases

Origin of bioinformatic/biological databases

  • The first bioinformatic/biological databases were constructed a few years after the first protein sequences began to become available.

  • The first protein sequence reported was that of bovine insulin in 1956, consisting of 51 residues.

  • Nearly a decade later, the first nucleic acid sequence was reported, that of yeast alaninetRNA with 77 bases

  • Just a year later, Dayhoff gathered all the available sequence data to create the first bioinformatic database.

  • The Protein Data Bank followed in 1972 with a collection of ten X-ray crystallographic protein structures

  • SWISSPROT protein sequence database began in 1987.

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Types of data available

Types of data available

Enormous amounts of data available publicly

– DNA/RNA sequence

– SNPs

– protein sequence

– protein structure

– protein function

– organism‐specific databases

– genomes

– gene expression

– biomolecular interactions

– molecular pathways

– scientific literature

– disease information

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Three central biological processes around which bioinformatics tools must be developed

Three Central biological processes around which bioinformatics tools must be developed:

  • DNA sequence determines protein sequence

  • Protein sequence determines protein structure

  • Protein structure determines protein function

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