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Bioinformatics

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Bioinformatics is the application of computer science and information science and technology to the field of life sciences.[1] Bioinformatics deals with algorithms, databases, data structures, Markov models[2], pattern matching[3] , web technologies and statistics. Bioinformatics involves various disciplines in the fields of science and biology and would not be possible without modern advances in computing hardware and software.[4] One of the main fields related to bioinformatics is computational molecular biology. In a broad sense, it consists of mathematical and computer science techniques to help solve problems in molecular biology. This field includes alignment of sequences, phylogeny and genome rearrangements.[5] One of the great successes in the field of bioinformatics was the Human Genome Project, completed in 2003.[2]

Some Subjects

A sequence alignment, produced by ClustalW, of two human zinc finger proteins, identified on the left by GenBank accession number.
  • Sequence alignment
  • Multiple sequence alignment
  • Phylogenetics
  • Genomics
  • Proteomics
  • Systems biology[6]
  • Structural bioinformatics and drug discovery
  • Modelling biological systems
  • Prediction of protein structure
  • Molecular Interaction, Docking algorithms
  • Analysis of gene expression and protein expression
  • Analysis of regulation
  • Computational evolutionary biology
  • DNA Sequencing[7]

Databases

  • GenBank e GenPept
  • RefSeq
  • UniProt/Swiss-Prot
  • EMBL
  • ENTREZ

Software commonly used in bioinformatics

Software Resource Description License
BioPerl http://bioperl.org A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications Artistic License and GPL
BioPython http://biopython.org Non-commercial Python tools for computational molecular biology, as well as bioinformatics Biopython License
BioRuby http://bioruby.open-bio.org A package of Open Source Ruby code for DNA and protein sequence analysis, alignment, database parsing, and other Bioinformatics tools GPL
R http://www.r-project.org Programming language and software environment for statistical computing and graphics. GPL
Basic Local Alignment Search Tool (BLAST) http://blast.ncbi.nlm.nih.gov/Blast.cgi An algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences Public Domain
ClustalW http://www.clustal.org A multiple sequence alignment computer program Free for academic users
Dendroscope http://www.dendroscope.org An interactive computer software program written in Java for viewing Phylogenetic trees Free use, but not open source
EMBOSS http://emboss.sourceforge.net A free open source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community GPL and LGPL
FASTA http://fasta.bioch.virginia.edu A DNA and protein sequence alignment software package Free for academic users
Molecular Evolutionary Genetics Analysis (MEGA) http://www.megasoftware.net A software to aid scientists and students in making dendrograms, or phylogenetic trees using nucleotide or protein sequences Freely available
PAUP http://paup.csit.fsu.edu/ A computational phylogenetics program for inferring evolutionary trees (phylogenies) Proprietary software
PHYLIP http://evolution.genetics.washington.edu/phylip/getme.html A free computational phylogenetics package of programs for inferring evolutionary trees (phylogenies) Freely available


References

  1. Ramsden, Jeremy J (2009). Bioinformatics: An Introduction (2nd ed.). London: Springer. p. 2. ISBN 978-1-84800-256-2. 
  2. 2.0 2.1 Sharma, Kal Renganathan (2009). Bioinformatics: Sequence Alignment and Markov Models. New York: McGraw-Hill. p. 1. ISBN 978-0-07-159306-9. 
  3. Gusfield, Dan (1997). Algorithms on Strings Trees and Sequences:Computer Science and Computational Biology. Cambridge: Cambridge University Press. p. 1-84. ISBN 0-521-58519-8. 
  4. Lesk, Arthur M (2008). Introduction to Bioinformatics (3rd ed.). Oxford: Oxford University Press. p. 16. ISBN 978-0-19-920804-3. 
  5. Setubal, João; Meidanis, João (1997). Introduction to Computational Molecular Biology. Boston: PWS Publishing Company. p. xi. ISBN 0-534-95262-3. 
  6. V. Maly, Ivan, ed. (2009). Systems Biology. New York: Humana Press. pp. 512. ISBN 978-1-934115-64-0. 
  7. Alphey, Luke (1997). DNA Sequencing:From Experimental Methods to Bioinformatics. New York: Springer/BIOS Scientific Publishers. pp. 206. ISBN 0-387-91509-5. 

Further reading