What is Bio-informatics?
Bio-informatics is a newly emerging interdisciplinary research area which may be defined as the interface between biological and computational sciences. Thus, the people working in this field in most cases either have a training in biology or computer science, and they learned about the other field by dealing with problems or using the tools of the other one. And although the term 'Bio-informatics' is not really well-defined, you could say that this scientific field deals with the computational management of all kinds of biological information, whether it may be about genes and their products, whole organisms or even ecological systems. Most of the Bio-informatics work that is being done deals can be described as analyzing biological data, although a growing number of projects deal with the organization of biological information. As a consequence of the large amount of data produced in the field of molecular biology, most of the current Bio-informatics projects deal with structural and functional aspects of genes and proteins. Many of these projects are related to the Human Genome Project.
First, the data produced by the thousands of research teams all over the world are collected and organized in databases specialized for particular subjects. Well-known examples are: GDB (Genome Data Base). , SWISS-PROT , GenBank , and PDB (Protein Data Bank). In the next step, computational tools are needed to analyse the collected data in the most efficient manner.
One example for such an integration effort is the GeneCards encyclopedia,. This resource contains data about human genes, their products and the diseases in which they are involved. (a process similar to "data mining").
Bio-Informatics: A computational approach to molecular biology
Bio-informatics has been the latest buzzword in the business and scientific community, the hype for this emerging field has been increasing day by day, more and more educational organizations have already added this name to their academic profiles.
If you were a computer-programmer, bio-informatics skills would enable you to make software for biological applications and if you were biologist, bio-informatics would probably be the best tool to speed up your work just by using a computer with an internet connection. On an over all, bio-informatics is a very important tool for any one who is serious about computing biological processes.
"Bio informatics is a science of solving biological problem using a mathematical and computational approach."
Many of us confuse Bio-informatics with that of Bio-computing; fundamentally it's a complete different field. Bio-computing or molecular computing is applying biology to solve complex and computationally almost impossible problems using biology, the best example is the famous 'Traveling sales man problem' which was treated computationally impossible to solve.// Bio-informatics a very new field, it has been hardly five years since this science has come into existence in a common man's life. It is a mathematical and computational approach, you need to know mathematics to actually understand bio-informatic application. Fundamental knowledge of molecular biology is also necessary to learn bio-informatics. Molecular biology is a branch of biology which primarily deals with functions, characteristics and structures of mainly three major macro-molecules DNA,RNA and Proteins.
Protecting Bio-informatics Tools :
Bio-informatics involves the use of computer software to gather, sort, and analyze biological data – often with a goal of finding "drug gable targets" for pharmaceutical R&D. It has not always been clear which form of legal protection (primarily, copyright or patents) provides the best value for a bio-informatics product, given, in particular, the considerable doubt and confusion in the European Union as to the validity of software patents. However, recent developments in the European Union with respect to software patents, coupled with industry trends in the US as well as Europe, suggest that bio-informatics companies should give patent protection a very close look.
Genomes to Life
The revolution in biology triggered by the Human Genome Project now promises far-reaching benefits.
Today, scientists have in hand the complete DNA sequences of genomes for many organisms — from microbes to plants to humans. The U.S. Department of Energy's Genomes to Life program will use the new genomic data and high-throughput technologies for studying the proteins encoded by the genome to explore the amazingly diverse natural capabilities in microbes. These can be exploited to help solve DOE mission challenges in
- Underlying goals of the Genomes to Life program that will enable these benefits are to Identify the protein machines that carry out critical life functions,
- Characterize the gene regulatory networks that control these machines,
- Explore the functional repertoire of complex microbial communities in their natural environments to provide a foundation for understanding and using their remarkably diverse capabilities to address DOE missions, and Develop the computational capabilities to integrate and understand these data and begin to model complex biological systems.
Features
- Data Integration
- Data export to excel and other formats
- Import and integration from diverse sources:
- Sequence data: Genbank, FASTA formatted files, Swissprot format
- Gene Ontology
- PDB
- KEGG
- Method Integration
- Methods from various disciplines for analysis of
- Sequence
- Structure
- Expression data
- Taxonomy and Phylogeny
- Metabolic pathways
- Workflows
- Automatic checking of data compatibility
- Background execution of workflows
- Available methods:
- Bio-informatics
- Blast and Psi-Blast
- Sequence repeat detection
- Function analysis for cluster of sequences
- Match sequence profiles and regular expressions
- Expression matrix processing: Completion, Normalization, Filtering and Masking
- Mapping of expression data to metabolic pathways, Gene Ontology
- Metabolic pathway reconstruction
- General
- Vector operations
- Sorting
- Shuffling
- Statistics (average, mean, etc.)
- Visual Orientation
- Graphical workflow representation
- Drag n drop workflow construction
- Hierarchical tabular viewers
- Diverse graphical viewers for biological data and workflow results
- Advantages
- Shallow learning curve thanks to visual programming
- Unified data structure
- Expandability through script language (python)
- Scalability from desktop to corporation
- Company-wide sharing of results and methods
The Daphnia Genomics Consortium (DGC) is an international network of investigators committed to mounting the freshwater crustacean Daphnia as a model system for evolutionary / ecological genetics and genomics
Dictyostelium discoideum genome annotation and analysis portal; specialized Dictyostelium sequence and function annotaton database.
Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes.
- MIPS:
Munich Information Centre for Protein Sequences projects include: fungal genome analysis, plant genome Bio-informatics, structural genomics, proteomics and genome annotation; databases include: Sputnik, MosDB, and PEDANT.
Parasite genome databases and genome research resources.
Genomic and cDNA library screening (human, mouse, dog, pig) is provided free to Canadian academic researchers with a nominal clone retrieval fee; includes Research Genetics, NIA/NIH and RIKEN cDNAs.
Provides a rapid and reliable display of any requested portion of the SARS genome at any scale, together with dozens of aligned annotation tracks.
Integrated Bio-informatics Software
GCG :-
GCG is one of the earliest integrated Bio-informatics system. It maintains more than 70 Bio-informatics data analysis tools, which are based on published algorithms from fields of mathematical and computational biology. In additions to running these programs individually, GCG allows the data flow among them. By using these tools, scientists can accomplish the following tasks:
- Sequence Comparison
- Database Searching and Retrieval
- DNA/RNA Secondary Structure Prediction
- Editing and Publication
- Evolution Analysis
- Fragment Assembly
- Gene Finding and Pattern Recognition
- Importing and Exporting Files in Different Formats
- Mapping
- Primer Selection
- Protein Analysis
- Translation
ICBR maintains a GCG server and keeps updated with NCBI and EBI databases. We support command line GCG. It gives the users quick and reliable analysis results. Regular GCG workshops are held once every year.
Biocatalog :-
The Biocatalog is a software directory of general interest in molecular biology and genetics. lists the databases DNA, Proteins, Alignments, Genomes, Genetic, Mapping, Molecular Evolution, Molecular graphics, databases, server.
BioTools (GeneTool & PepTool) :-
BioTools Suite includes GeneTool and PepTool for nucleotide and peptide sequence analysis respectively. Compared to GCG, BioTools has the most user-friendly interface. It covers almost all routine Bio-informatics jobs while the analysis function is less powerful than GCG. However, we find BioTools is a very good software for Bio-informatics novices and basic analysis. It's much better developed and more reliable than those freeware you can get from the Internet. Here we list some features of BioTools.
- Chromatogram Analysis and Sequence Assembly
- Database Reference Search and BLAST Search
- Multiple Alignment
- Vector Construct
- Primer Design
- Biochemistry Statistics of Nucleotide & Protein Sequence
- Translation
- Restriction Map
BioEdit
In addition to a sequence alignment editor, BioEdit is also connected with a wide range of free Bio-informatics programs on the Internet. The topics cover from BLAST search to promoter prediction. If you want to get some freeware, BioEdit is a good one you may want to have a look at.
Real world applications of Bio-informatics:
At present all drugs on the market target only about 500 proteins. With an improved understanding of disease mechanisms and using computational tools to identify and validate new drug targets, more specific medicines that act on the cause, not merely the symptoms, of the disease can be developed. These highly specific drugs promise to have fewer side effects than many of today's medicines.
Clinical medicine will become more personalised with the development of the field of pharmacogenomics. This is the study of how an individual's genetic inheritence affects the body's response to drugs. At present, some drugs fail to make it to the market because a small percentage of the clinical patient population show adverse affects to a drug due to sequence variants in their DNA.
With the specific details of the genetic mechanisms of diseases being unravelled, the development of diagnostic tests to measure a persons susceptibility to different diseases may become a distinct reality. Preventative actions such as change of lifestyle or having treatment at the earliest possible stages when they are more likely to be successful, could result in huge advances in our struggle to conquer disease.
In the not too distant future, the potential for using genes themselves to treat disease may become a reality. Gene therapy is the approach used to treat, cure or even prevent disease by changing the expression of a persons genes. Currently, this field is in its infantile stage with clinical trials for many different types of cancer and other diseases ongoing.
2. Microbial genome applications :-
Deinococcus radiodurans is known as the world's toughest bacteria and it is the most radiation resistant organism known. Scientists are interested in this organism because of its potential usefulness in cleaning up waste sites that contain radiation and toxic chemicals.
Increasing levels of carbon dioxide emission, mainly through the expanding use of fossil fuels for energy, are thought to contribute to global climate change. Recently, the DOE (Department of Energy, USA) launched a program to decrease atmospheric carbon dioxide levels. One method of doing so is to study the genomes of microbes that use carbon dioxide as their sole carbon source.
Scientists are studying the genome of the microbe Chlorobium tepidum which has an unusual capacity for generating energy from light
The archaeon Archaeoglobus fulgidus and the bacterium Thermotoga maritima have potential for practical applications in industry and government-funded environmental remediation. These microorganisms thrive in water temperatures above the boiling point and therefore may provide the DOE, the Department of Defence, and private companies with heat-stable enzymes suitable for use in industrial processes
Scientists have been examining the genome of Enterococcus faecalis-a leading cause of bacterial infection among hospital patients. They have discovered a virulence region made up of a number of antibiotic-resistant genes that may contribute to the bacterium's transformation from a harmless gut bacteria to a menacing invader. The discovery of the region, known as a pathogenicity island, could provide useful markers for detecting pathogenic strains and help to establish controls to prevent the spread of infection in wards.
The sequencing of the genomes of plants and animals should have enormous benefits for the agricultural community. Bioinformatic tools can be used to search for the genes within these genomes and to elucidate their functions. This specific genetic knowledge could then be used to produce stronger, more drought, disease and insect resistant crops and improve the quality of livestock making them healthier, more disease resistant and more productive.
Sequencing projects of many farm animals including cows, pigs and sheep are now well under way in the hope that a better understanding of the biology of these organisms will have huge impacts for improving the production and health of livestock and ultimately have benefits for human nutrition
Analysing and comparing the genetic material of different species is an important method for studying the functions of genes, the mechanisms of inherited diseases and species evolution. Bioinformatics tools can be used to make comparisons between the numbers, locations and biochemical functions of genes in different organisms.
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