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BIOINFORMATICS

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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  1. BIOINFORMATICS Ayesha MasrurKhan Spring 2013 Lec-2

  2. 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." Lec-2

  3. 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. Lec-2

  4. 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. Lec-2

  5. 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. Lec-2

  6. 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 Lec-2

  7. 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. Lec-2

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  11. 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. Lec-2

  12. 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. Lec-2

  13. 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 Lec-2

  14. 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 Lec-2

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