Software tools

 The computational biology tool best-known among biologists is probably BLAST, an algorithm for searching large databases of protein or DNA sequences. NCBI provides a popular implementation that searches their massive sequence databases. Bioinformatic meta search engines (Entrez, Bioinformatic Harvester) help finding relevant information from several databases. There are also free Web-based software designed for structural bioinformatics such as [1] STING.

Computer scripting languages such as Perl and Python are often used to interface with biological databases and parse output from bioinformatics programs. Communities of bioinformatics programmers have set up free/open source projects such as EMBOSS, Bioconductor, BioPerl, BioLinux, BioPython, BioRuby, and BioJava which develop and distribute shared programming tools and objects (as program modules) that make bioinformatics easier.

There are several integrated software workbenches consisting of many free/open source tools described above. Taverna, an open-source bioinformatics workbench that utilises a workflow model of experimental design, is included as part of the myGRID package of e-science software. Quantum 3.1 is an example of the bioinformatics post-QSAR technology applying quantum and molecular physics instead of statistical methods. Genevestigator is an example of how large-scale gene expression microarray data is used to predict gene function based on contextual information.

More recently, SOAP-based interfaces have been developed for a wide variety of bioinformatics applications such as blast, fasta, EMBOSS, clustalw, t-coffee, MUSCLE and many others. These are available from the EBI at EBI Web Services.

References

• Baldi, P and Brunak, S, Bioinformatics: The Machine Learning Approach, 2nd edition. MIT Press, 2001. ISBN 0-262-02506-X

• Barnes, M.R. and Gray, I.C., eds., Bioinformatics for Geneticists, first edition. Wiley, 2003. ISBN 0-470-84394-2

• Baxevanis, A.D. and Ouellette, B.F.F., eds., Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, third edition. Wiley, 2005. ISBN 0-471-47878-4

• Claverie, J.M. and C. Notredame, Bioinformatics for Dummies. Wiley, 2003. ISBN 0-7645-1696-5

• Durbin, R., S. Eddy, A. Krogh and G. Mitchison, Biological sequence analysis. Cambridge University Press, 1998. ISBN 0-521-62971-3

• Gilbert, D. Bioinformatics software resources. Briefings in Bioinformatics, Briefings in Bioinformatics, 2004 5(3):300-304.

• Kohane, et al. Microarrays for an Integrative Genomics. The MIT Press, 2002. ISBN 0-262-11271-X • Lund, O. et al. Immunological Bioinformatics. The MIT Press, 2005. ISBN 0-262-12280-4

• Michael S. Waterman, Introduction to Computational Biology: Sequences, Maps and Genomes. CRC Press, 1995. ISBN 0-412-99391-0

• Mount, David W. Bioinformatics: Sequence and Genome Analysis Spring Harbor Press, May 2002. ISBN 0-87969-608-7

• Pachter, Lior and Sturmfels, Bernd. "Algebraic Statistics for Computational Biology" Cambridge University Press, 2005. ISBN 0-521-85700-7

• Pevzner, Pavel A. Computational Molecular Biology: An Algorithmic Approach The MIT Press, 2000. ISBN 0-262-16197-4

Major Research Areas Sequence analysis

Analysis of gene expression

Prediction of protein structure

Software tools