In this paper the idea is to provide an outline of the interesting area bioinformatics that play a key role in the major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, and the modeling of evolution.
The contents of the paper include introduction, definitions, history, software, tools, program applications, projects, applications in various areas and case studies.
Bioinformatics more properly refers to the creation and advancement of algorithms, computational and statistical techniques, and theory to solve formal and practical problems posed by or inspired from the management and analysis of biological data.
During the last ten years, molecular biology has witnessed an information revolution as a result both of the development of rapid DNA sequencing techniques and of the corresponding progress in computer based technologies which are allowing us to manage with this information overflow in increasingly efficient ways. The broad term that was coined in the mid 1980s to include computer applications in biological sciences is Bioinformatics. The bioinformatics the term can be considered to mean information technology applied to the management and analysis of biological data.
This has some implications in diverse areas, ranging from artificial intelligence and robotics to genome analysis.
Bioinformatics derives knowledge from computer analysis of biological data. It is a rapidly developing branch of biology and is highly interdisciplinary, using techniques and concepts from informatics, statistics, mathematics, chemistry, biochemistry, physics, and linguistics. It has many practical applications in different areas of biology and medicine.
Roughly, bioinformatics describes any use of computers to handle biological information. In practice the definition used by most people is narrower; bioinformatics to them is a synonym for "computational molecular biology"- the use of computers to characterize the molecular components of living things.
ORIGIN & HISTORY OF BIOINFORMATICS
Since from Mendel period, genetic record keeping have come a long way. The understanding of genetics has advanced remarkably in the last thirty years.
In 1988, the Human Genome organization (HUGO) was founded. This is an international organization of scientists involved in Human Genome Project. In 1989, the first complete genome map was published of the bacteria Haemophilus influenza. By 1991, a total of 1879 human genes had been mapped. In 1993, Genethon, a human genome research center in France Produced a physical map of the human genome. Three years later, Genethon published the final version of the Human Genetic Map.Bioinformatics was fuelled by the need to create huge databases, such as GenBank and EMBL and DNA Database of Japan to store and compare the DNA sequence data erupting from the human genome and other genome sequencing projects. Iiii
The use of software in biological applications has given a new dimension to the field of bioinformatics. There are number of simple stand-alone programs as well as complex integrated network version of the commercial software available. But keeping track of all the programmes is difficult task although it should not be taken as exhaustive list; it is useful to scientist/students from life science as well as bioinformatics stream.
This list includes Windows version, Linux and Mac version only. The criteria for selecting bioinformatics software's
• Software should be accessible to all, easy to use and should run on normal PC. Maximum concentrated on GUI interface and to some extent DOS commands to avoid command interface.
• Software list selected below to run some of common tasks in bioinformatics, which should be usable to person from varied fields from life sciences/molecular biology background.
• Last but not the least, software's should be easy to install with out complex commands.
EMBOSS (European Molecular Biology Open Software Suite) is a software-analysis package. It can work with data in a range of formats and also retrieve sequence data transparently from the Web. Extensive libraries are also provided with this package, allowing other scientists to release their software as open source. It provides a set of sequence-analysis programs, and also supports all UNIX platforms.
• A properly constructed toolkit for creating healthy bioinformatics applications or workflows.
• A comprehensive set of sequence analysis programs.
• All sequence and many alignment and structural formats are handled.
• Additional programming libraries for many other areas including string handling, pattern-matching, list processing and database indexing.
• Each application has the same style of interface so master one and you've mastered them all.
• The consistent user interface facillitates GUI designers and developers.
• There are no limits on the amount of data that can be processed. For the programmer, memory management for objects such as sequences and arrays is simplified.
Within EMBOSS you will find around hundreds of programs (applications) covering areas such as:
• Sequence alignment,
• Rapid database searching with sequence patterns,
• Protein motif identification, including domain analysis,
Bioinformatic tools are software programs that are designed for extracting the meaningful information from the mass of molecular biology / biological databases & to carry out sequence or structural analysis.Factors that must be taken into consideration when designing bioinformatics tools, software and programmes are:
• The end user (the biologist) may not be a frequent user of computer technology
• These software tools must be made available over the internet given the global distribution of the scientific research community
Major categories of bioinformatics tools:
Bioinformatics Tools can be classified as
• Homology and similarity tools.
• Protein functional analysis tools.
• Sequence analysis tools.
• Miscellaneous tools.
Iiiii Bioinformatics is done with sequence search programs like BLAST, sequence analysis programs, like the EMBOSS and Staden packages, structure prediction programs like THREADER or PHD or molecular imaging/modelling programs like RasMol and WHATIF.
Some examples of Bioinformatics Tools:
BLAST (Basic Local Alignment Search Tool) comes under the category of homology and similarity tools. It is a set of search programs designed for the Windows platform and is used to perform fast similarity searches regardless of whether the query is for protein or DNA. Comparison of nucleotide sequences in a database can be performed. Also a protein database can be searched to find a match against the queried protein sequence. NCBI has also introduced the new queuing
system to BLAST (Q BLAST) that allows users to retrieve results at their convenience and format their results multiple times with different formatting options.
Program applications in Bioinformatics:
Since research centers are scattered all around the globe ranging from private to academic settings, and a range of hardware and OSs are being used, Java is emerging as a key player bioinformatics
The BioJava Project is dedicated to providing Java tools for processing biological data which includes objects for manipulating sequences, dynamic programming, file parsers, simple statistical routines, etc
Since research centers are scattered all around the globe ranging from private to academic settings, and a range of hardware and OSs are being used, Java is emerging as a key player in bioinformatics.
BioJava:The BioJava Project is dedicated to providing Java tools for processing biological data which includes objects for manipulating sequences, dynamic programming, file parsers, simple statistical routines, etc.
BioPerl: The BioPerl project is an international association of developers of Perl tools for bioinformatics and provides an online resource for modules, scripts and web links for developers of Perl-based software.