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Muhammad Ali Hashmi FA12-R66-001 PhD Scholar CIIT, Abbottabad
1 Bioinformatics
Bioinformatics is also known as Computational Biology. It is an interdisciplinary field that develops and advances on different methods for storing, retrieving, organizing and analyzing biological/biochemical data. It might be appropriate to say that Computational Biology or Bioinformatics deals with the application of computers in solving problems of molecular biology/biochemistry. The major role of bioinformatics is to develop software tools to generate useful biological knowledge [1]. Bioinformatics has become a very important part of many areas of biochemistry and biology. Bioinformatics works in collaboration with experimental molecular biology and biochemistry. Bioinformatics techniques like image processing and signal processing allow extraction of useful results from large amounts of raw data. It helps in genome sequencing and genome annotation in the field of genetics and genomics. Its role in the analysis of gene expression and proteomics is very vital. It also aids in modeling and simulations of Deoxyribonucleic acid, ribonucleic acid, and the structures of different proteins and the molecular interactions within them [2]. Bioinformatics is actually a science which is a collection of different disciplines like biology, computer science, biochemistry, mathematics and engineering. Powerful computers are used to solve biological problems which were not so easy to process before. To store and organize biological data, different databases and information systems are used [3].
1.1 History
Paulien Hogeweg in 1978 introduced the term Bioinformatics which refer s to the study of information processes in biotic systems [4, 5]. This definition placed bioinformatics near to biophysics or biochemistry (biochemistry is the study of chemical processes in biological systems) [4]. Examples of relevant biological information processes studied in the early days of bioinformatics are the formation of complex social interaction structures by simple behavioral rules, and the information accumulation and maintenance in models of prebiotic evolution. One early contributor to bioinformatics was Elvin A. Kabat, who pioneered biological sequence analysis with his comprehensive volumes of antibody sequences released with Tai Te Wu between 1980 and 1991 [6]. Another significant pioneer in the field was Margaret Oakley Dayhoff, who has been hailed by David Lipman, director of the National Center for Biotechnology Information, as the "mother and father of bioinformatics" [7]. The most important achievement of bioinformatics is the human genome project which was mapped in 2001.
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Sequence/Sequence Annotation
GenBank GenBank Stats Ensembl EntrezGene UCSC-GoldenPath RefSeq SwissProt UniProt TrEMBL GeneCards Mouse genome (MGD) http://www.ncbi.nlm.nih.gov/BLAST/ http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.html http://www.ensembl.org/ http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db = gene http://www.genome.ucsc.edu/cgi-bin/hgGateway http://www.ncbi.nlm.nih.gov/RefSeq/ http://us.expasy.org/sprot/ http://www.pir.uniprot.org/ http://www.ebi.ac.uk/trembl/index.html http://bioinfo.weizmann.ac.il/cards/index.shtml database http://www.informatics.jax.org/menus/allsearch_menu.shtml http://rgd.mcw.edu/ http://magpie.ucalgary.ca/ http://symatlas.gnf.org/SymAtlas/ http://www.imm.ki.se/CYPalleles/ P-450 www.icgeb.org/p450/ P-450 http://medicine.iupui.edu/flockhart/table.htm
Rat genome database (RGD) MAGPIE/BLUEJAY SymAtlas CypAlleles DB Directory of containing systems Cytochrome interaction table Human transporter (HMTD) Transporters page Muhammad Ali Hashmi
Human ABC transporters http://nutrigene.4t.com/humanabc.htm database SNPs and Mutations The SNP Consortium JSNP HGVbase http://snp.cshl.org/ http://snp.ims.u-tokyo.ac.jp/ hgvbase.cgb.ki.se/
Main metabolic pathways http://home.wxs.nl/~pvsanten/mmp/mmp.html Web page The Medical Biochemistry http://web.indstate.edu/thcme/mwking/ Page UM-BBD http://umbbd.ahc.umn.edu/
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protein structure has been determined by purifying a protein, crystallizing it, and then bombarding it with X-rays. The X-ray diffraction pattern from the bombardment is recorded electronically and analyzed using software that creates a rough draft of the 3D structure. Biological scientists and crystallographers then tweak and manipulate the rough draft considerably. The resulting spatial coordinate file can be examined using modeling- structure software to study the gross and subtle features of the protein's structure [16].
3 Conclusion
Bioinformatics is a very helpful field as it makes such tools which provide the full information about the proteins and gene families and researchers can use this information for various applications for example drug target and drug discovery in particular.
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4 References
1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. Waterman, M.S., Introduction to Computational Biology: Maps, Sequences, and Genomes. 1995: Chapman & Hall/crc. Mount, D.W., Bioinformatics: sequence and genome analysis. 2004: Cold Spring Harbor Laboratory Press. Claverie, J.M. and C. Notredame, Bioinformatics For Dummies. 2011: Wiley. Hogeweg, P., The Roots of Bioinformatics in Theoretical Biology. PLoS Comput Biol, 2011. 7(3): p. e1002021. Hogeweg, P., Simulating the growth of cellular forms. SIMULATION, 1978. 31(3): p. 90-96. Moody, G., Digital Code of Life: How Bioinformatics is Revolutionizing Science, Medicine, and Business. 2004: Wiley. Johnson, G. and T. Te Wu, Kabat database and its applications: 30 years after the first variability plot. Nucleic acids research, 2000. 28(1): p. 214-218. Wishart, D.S., Bioinformatics in Drug Development and Assessment. Drug Metabolism Reviews, 2005. 37(2): p. 279-310. Kramer, R. and D. Cohen, Functional genomics to new drug targets. Nat Rev Drug Discov, 2004. 3(11): p. 965-972. Butte, A., The use and analysis of microarray data. Nat Rev Drug Discov, 2002. 1(12): p. 951-960. Onyango, P., The role of emerging genomics and proteomics technologies in cancer drug target discovery. Current Cancer Drug Targets, 2004. 4(2): p. 111-124. Comess, K. and M. Schurdak, Affinity-based screening techniques for enhancing lead discovery. Current opinion in drug discovery & development, 2004. 7(4): p. 411. Ackermann, B.L., M.J. Berna, and A.T. Murphy, Recent advances in use of LC/MS/MS for quantitative high-throughput bioanalytical support of drug discovery. Current topics in medicinal chemistry, 2002. 2(1): p. 53-66. Carlton, J., The Plasmodium vivax genome sequencing project. Trends in Parasitology, 2003. 19(5): p. 227-231. Goldstein, D.B., S.K. Tate, and S.M. Sisodiya, Pharmacogenetics goes genomic. Nature Reviews Genetics, 2003. 4(12): p. 937-947. Smith, C., Bioinformatics, Genomics, and Proteomics. Scientist, 2000. 14: p. 23-26. Page 8