Bioinformatics, Genomics, Proteomics
John D. FurberMaster of Science, Biological Sciences, University of California, Irvine.
Bachelor of Arts, Physics and Mathematics, University of California, Santa Cruz.
[John D. Furber home page]
Bioinformatics and GenomicsBioinformatics is the scientific discipline of discovering biological functions through analysis of molecular sequence information from DNA, RNA, or proteins. Tasks include:
Bioinformatics is sometimes called "Functional Genomics." Genomics is study of entire genomes, the complete set of DNA sequences of cells and organisms. The human genome consists of 3 billion pairs of DNA nucleotides (base-pairs) which encode an estimated 50,000 to 120,000 genes. Celera Genomics has a tutorial called What's a Genome?
- Comparing an interesting or newly discovered "Query Sequence" with a large database of previously discovered sequences.
- Looking for similar sequence motifs (patterns) among a group of similar protein or nucleic acid domains. Similar sequence motifs are often indicative of similar local structural form and function.
- Predicting 3-dimensional molecular structures from 1-dimensional sequence data.
- Drug discovery and drug design.
Proteomics is the study of all of the proteins in a cell, tissue, or organism, rather than studying them one at a time. The interactions of the proteins are very important. Current proteomics techniques involve electrophoretic separation on a 2-dimensional polyacrylamide gel. Other analytical techniques under development make use of antibody affinities or physical and chemical properties of protein sequences. Bioinformatics also uses the gene sequences to predict what proteins should be present.
Genomics tasks include:
These problems can be highly complex, and some of the databases are very large, requiring the use of computers with sophistocated algorithms. Several of these tools and databases are publicly available on the WWW.
- Determining the DNA sequence of the genome and of all the genes within the genome.
- Mapping the locations of genes and genetic diseases.
- Exploring the organization of genes within the genome, including control elements, silencing, and evolutionary relationships among species.
Protein Families, Motifs, and Domains
- NRCAM - The National Resource for Cell Analysis and Modeling is a national resource center supported by the National Center for ResearchResources (NCRR), at the National Institutes of Health (NIH). It is the home of the Virtual Cell.
- The NIH Center for Molecular Modeling http://cmm.info.nih.gov/modeling/
- The Digital Human Project of the Federation of American Scientists "is working to build a collaborative community of information and biological scientists to accelerate development and use of biomedical simulation for research and learning. Our goal is development of a framework that will permit researchers to collaborate, share their work, and test each other's systems." http://www.fas.org/main/content.jsp?formAction=325&projectId=12
- The Physiome Project web site has not been updated recently. It's major long-range goal "is to understand and describe the human organism, its physiology and pathophysiology quantitatively, and to use this understanding to improve human health.
- The BioJava Project is an international association of developers of Java tools for bioinformatics.
- The Bioperl Project is an international association of developers of public domain Perl programming tools for Computational Molecular Biology.
- The BiopythonProject is an international association of developers of Python tools for bioinformatics.
- The Bioxml Project is an international association of developers of XML tools for bioinformatics.
- The Open lab is an international collaboratory for open-sources bioinformatics R&D.
- The International Society for Computational Biology is dedicated to advancing the scientific understanding of living systems through computation. Its emphasis is on the role of computing and informatics in advancing molecular biology.
- The Pacific Symposium on Biocomputing 2000 was held in Hawaii in January 2000. http://www.cgl.ucsf.edu/psb/
- The Institute of Theoretical Dynamics at the University of California, Davis, has projects in Computational Biology and Nonlinear Dynamics in Biology.
Contact information:John D. Furber
E-mail: johnfurber at aol.com
[John D. Furber home page]
© 2000 - 2004 by John D. Furber. All rights Reserved.