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Biology is in the middle of a major paradigm shift driven by computing technology. Although it is already an informational science in many respects, the field has been rapidly becoming much computational and analytical. Rapid progress in genetics and biochemistry research combined with the tools provided by modern biotechnology has generated massive volumes of genetic and protein sequence data. Bioinformatics has been defined as a means for analysing, comparing, graphically displaying, modeling, storing, systemising, searching, and ultimately distributing biological discipline that information, which includes sequences ,structures, function, and phylogeny. Thus bioinformatics may be defined as a generates computational tools, databases, and methods to support genomic and post genomic research. It comprises the study of DNA structure and function, gene and protein expression, protein production, structure and function, genetic regulatory systems, and clinical applications. Bioinformatics needs the expertise from Computer Science, Mathematics, Statistics, Medicine, and Biology. Bioinformatics is the application of computer technology to the management of biological information. Computers are used to together store, analyse and integrate biological and genetic information which can,then, be applied to the gene-based drug discovery and development. more
Definition of Bioinformatics
Bioinformatics is the analysis of biological information using computers and statistical techniques. The science of developing and utilizing computer databases and algorithms to accelerate and enhance biological research. Bioinformatics is more of a tool than a discipline, the tools for analysis of biological Data.
The National Center for Biotechnology Information (NCBI 2001) defines bioinformatics as:
is the field of science in which biology, computer science,
and information technology merge into a single discipline. There are three important sub-disciplines within bioinformatics: the development of new algorithms and statistics with which to assess relationships among members of large data sets. The analysis and interpretation of various types of data including nucleotide and amino acid sequences, protein domains, and protein structures and the development and implementation of tools that enable efficient access and management of different types of information."
The application of computer technology to the management of biological information. Specifically, it is the science of developing computer databases and algorithms to facilitate and expedite biological research. Bioinformatics is being used largely in the field of human genome research by the Human genome Project that has been determining the sequence of the entire human genome (about 3 billion base pairs) and is essential in using genomic information to understand diseases. It is also used largely for the identification of new molecular targets for drug discovery.
The three terms bioinformatics, computational biology and bioinformation infrastructure are often times used interchangeably. These three may be defined as follows: 1. bioinformatics refers to database-like activities, involving persistent sets of data that are maintained in a consistent state over essentially indefinite periods of time;
2. computational biology encompasses the use of algorithmic tools to facilitate biological analyses; while 3. bioinformation infrastructure comprises the entire collective of information management systems, analysis tools and communication networks supporting biology. Thus, the latter may be viewed as a computational scaffold of the former two.
Bioinformatics 4 4 .
is extremely sketch and inaccurate. Biological Science and computational Science. B. and before the discovery of genetic inheritance by G. Mendel in 1865. Mendel illustrated that the 5 . Here is the data of historical events for both biology and computer sciences. History of Bioinformatics The Modern bioinformatics is can be classified into two broad categories.Bioinformatics 5 . This was the start of Bioinformatics history. is known as the "Father of Genetics". He did experiment on the crossfertilization of different colors of the same species. He carefully recorded the data and analyzed the data. The history of biology in general. Gregor Mendel.C.
Ernst Haeckel (Häckel) outlined the essential elements of modern zoological classification. 7. The understanding of genetics has advanced remarkably in the last thirty years. He argued for an organic origin of fossils. two important things happened in the field of genomics. BioInformatics Events Robert Hooke published Micrographia. Richard Owen elaborated the distinction of homology andanalogy. The chromosome theory of heredity is proposed by Sutton and Boveri. Austria.H. as shown by Lederberg and Tatum. Here are some of the major events in bioinformatics over the last several decades. and suggested a plausible mechanism for their formation.600 kinds of plants. established the theory of genetic inheritance. A new technique. In 1972. Annie Chang and Herbert Boyer produced the first recombinant DNA organism. Gregory Mendel (1823-1884). was coined. Morgan). comparing their microscopic structure to that of the living organisms they resembled. The events listed in the list occurred long before the term. it is the 1990s when the INTERNET arrived when the full fledged bioinformatics field was born. 4) Genetic material can be transferred laterally between bacterial cells. is introduced by Tiselius for separating proteins in solution. No. He also described microscopic examinations of fossilized plants and animals. Ser. In that same year. Sweden. Uppsala University. Paul berg made the first recombinant DNA 6 molecule using ligase. John Ray. John Ray's in his book "Historia Plantarum" catalogued and described 18. IV. However. Tiselius. In 1973. The advancement of computing in 1960-70s resulted in the basic methodology of bioinformatics. Antoni van Leeuwenhoek discovered bacteria. His book gave the first definition of species based upon common descent. First ever linkage map created by Columbia undergraduate Alfred Sturtevant (working with T. 1665 1683 1686 1843 1864 1865 1902 1962 1905 1913 1930 1946 6 . Pauling's theory of molecular evolution The word "genetics" is coined by William Bateson. "bioinformatics". electrophoresis.Bioinformatics inheritance of traits could be more easily explained if it was controlled by factors passed down from generation to generation. Stanley Cohen. working independently. "The moving-boundary method of studying the electrophoresis of proteins" (published in Nova Acta Regiae Societatis Scientiarum Upsaliensis. Vol. described the cellular structure of cork.
The A. 7 .3 Mbp) is published. PubMed The genome for Pseudomonas aeruginosa (6. Hinxton. Tombor B. The large-scale organization of metabolic networks. Oltvai ZN. UK EMBL European Bioinformatics Institute. Nature 2000 Oct 5. Hinxton.Bioinformatics 1952 1961 1965 1970 1977 7 Alfred Day Hershey and Martha Chase proved that the DNA alone carries genetic information. Matthew Meselson. thaliana genome (100 Mb) is secquenced.407(6804):651-4. UK First bacterial genomes completely sequenced Yeast genome completely sequenced PSI-BLAST Worm (multicellular) genome completely sequenced Fly genome completely sequenced Jeong H. Barabasi AL. This was proved on the basis of their bacteriophage research. identify messenger RNA. Sidney Brenner. François Jacob. Albert R. Margaret Dayhoff's Atlas of Protein Sequences Needleman-Wunsch algorithm DNA sequencing and software to analyze it (Staden) 1981 1981 1982 1982 1983 1985 1988 1988 1990 1991 1993 1994 1995 1996 1997 1998 1999 2000 2000 2000 2001 Smith-Waterman algorithm developed The concept of a sequence motif (Doolittle) GenBank Release 3 made public Phage lambda genome sequenced Sequence database searching algorithm (Wilbur-Lipman) FASTP/FASTN: fast sequence similarity searching National Center for Biotechnology Information (NCBI) created at NIH/NLM EMBnet network for database distribution BLAST: fast sequence similarity searching EST: expressed sequence tag sequencing Sanger Centre. The human genome (3 Giga base pairs) is published.
Pharmacogenomics: It is the application of genomic approaches and technologies to the identification of drug targets. medical. mathematical modelling and computational simulation techniques to the study of biological.( or) application of computational tools and approaches for expanding the use of biological. and social systems. Genomics: Genomics is any attempt to analyze or compare the entire genetic complement of a species .of course possible to compare genomics by comparing more or less representative subsets of genes within genomes. archive. analyze.structure and function.It is . or visualize such data. Chemical informatics: Computer assisted storage. Computational Biology: The development and application of data analytical and theoretical methods. retrieval and analysis of chemical information from data to chemical knowledge.In short.Bioinformatics 8 DEFINITIONS RELATED TO BIOINFORMATICS : Bioinformatics: Research. pharmacogenomics is using genetic information to predict whether a drug will help make a patient well or sick. 8 . organize. development. Pharmacogenetics: It is the study of how the actions of and reactions to drugs vary with the patients genes.behavioral or health data. behavioral. including those to acquire store. Proteomics: It is the study of proteins-their location.
the fruit fly and the bacterium E. The second aim is to develop tools and resources that aid i n the analysis of data. the Protein Data Bank for 3D macromolecular structures. the information stored in these databases is essentially use-less until analysed. at its simplest bioinformatics organises data in a way that allows researchers to access existing information and to submit new entries as they are produced. Pharmacoinformatics: It concentrates on the aspects of bioinformatics dealing with drug discovery. Development of such resources dictates expertise in computational theory as well as a thorough under-standing of biology. e.coli.Bioinformatics 9 Comparative genomics: The study of human genetics by comparisons with model organisms such as mice. Thus the purpose of bioinformatics extends much further. This needs more than just a simple text-based search and programs such as FASTA and PSIBLAST must consider what comprises a biologically significant match.g. it is of interest to compare it with previously characterised sequences. For example. AIMS OF BIOINFORMATICS : The aims of bioinformatics include: First. 9 . having sequenced a particular protein. While data-curation is an essential task. Biophysics: An interdisciplinary field which applies techniques from the physical sciences to understanding biological structure and function.
Bioinformatics 10 The third aim is to use these tools to analyse the data and interpret the results in a biologically meaningful manner. we can now conduct global analyses of all the available data with the aim of un-covering common principles that apply across many systems and highlight novel features. To coordinate worldwide efforts to gather biological data 10 . The National centre for biotechnology Information(NCBI) in the United states and the European Bioinformatics institute(EBI) in England are two main life science servers responsible for dealing with this data. biological studies examined individual systems in detail and frequently compared them with a few that are related. To facilitate usage of the database and analytical software available to the scientific community. INFORMATION NETWORKS: Computational tools and databases are essential to the management and identification of suitable patterns found by using exponentially growing volume of biological data. the US senate recognised the need for computerused data processing in the biomedical and biochemical field and passed legislation that helped to establish NCBI at the National library of medicine(NLM) NCBI’s four main tasks are: To crate automated machines that can analyse and store data pertaining to molecular biology. Traditionally. National centre for Biotechnology Information (NCBI) In November 1988.genetics and biochemistry. In bioinformatics.
g:PIR’s complete database which consists of PIR!+PIR2+PIR3. 1. It tasks and goals are similar to those of NCBI and include : Bioinformatics tracking technology Research and development of bioinformatics software Training and supporting its subscribers Relevant bioinformatics services.Bioinformatics To conduct research in computerised analysis of structure function relationships for key biological molecules. Databases at EBI: EMBL database SWISS.PROT database dbEST&dbSTS PDB NDB 11 . 11 Databases supported by NCBI: Protein sequence: These are experimentally sequenced proteins and translated nucleotide sequences from nucleotide libraries. Redundant nucleotide sequence databases-Eg. dbEST European Bioinformatics institute(EBI): EBI is an outstation of the European molecular biology laboratory(EMBL) located at Hinxton. redundant protein sequence databases –E. Nucleotide sequence: These are DNA and RNA sequences derived from less automated sequencing projects I. England.
FASTA etc. Database Management Systems Learn Oracle and MySQL (Free Database Server) which is extensively used for store gigabytes of biotech data for further analysis. Learn to use sequence analysis and molecular modeling software. Some of the molecular biology packages are GCG. Java and HTML should be known by Bioinformatician. Experience with one or more of Molecular Biology software packages. 1. Here is the important topics very essential to enter in this profession.Bioinformatics IMGT database 12 Skills Required to become successful Bioinformatician: As mentioned earlier Bioinformatics profession requires wide range and it is not possible to learn all of them. 6. Molecular Biology 2. Central Dogma of molecular biology 3. BIOLOGICAL DATABASES : 12 . 4. Computer Programming Language like C/C++. BLAST. This platform. Perl or Python. its very important to learn these operating system. 7. Learn Unix or Linux Since these days Unix or Linux (Free open source) is extensively used in biotechnology for is robustness and available tools & software for 5.
often. a record associated with a nucleotide sequence database typically contains information such as contact name. and.Easy access to the information. A simple database might be a single file containing many records. query.organized body of persistent data usually associated with computerized software designed to update. two additional requirements must be met: 1. For example. literature citations associated with the sequence.Bioinformatics 13 A biological database is alarge . and retrieve components of the data stored within the system. the input sequence with description of the type of molecule. For researchers to benefit from the data stored in a database. each of which includes the same set of information. and 13 . the scientific name of the source organism from which it waisolated.
RNA and DNA are the proteins that store the 14 .A method for extracting only that information needed to answer a specific biological question. a lot of bioinformatics work is concerned with thetechnology of databases. These data bases include both "public" repositories of gene data like Gene Bank or the Protein Data Bank (the PDB) and private databases like those used by research groups involved in gene mapping projects or those held by biotech companies.Bioinformatics 2. 14 Currently. Making such databases accessible via open standards like the Web is very important since consumers of bioinformatics data use a range of computer platforms: from the more powerful and forbidding UNIX boxes favoured by the developers and curators to the far friendlier Macs often found populating the labs of computerwary biologists.
Swiss-Prot 2. Nuclear Receptor Database (NucleaRDB) 5. European Molecular Biology Laboratory (EMBL) Composite Databases 1.Bioinformatics 15 hereditary information about an organism. GenBank 2. Catalogue of Databases (DBCAT) Other Databases 1. Structural Classification of Proteins 3. Architecture. National Center for Biotechnology Information (NCBI) 2. G-Protein Coupled Receptor Database (GPCRDB) 4. Protein Structure Database: 1. Topology and Homologous super family Protein Sequence Database • Primary Database 1. Receptor-Ligand Database (ReliBase) 2. Restriction Enzyme Database (REBASE) 3. Protein Data Bank (PDB) 2. which can be analyzed by biologists with the help of bioinformatics tools and databases. Literature Database – PubMed 15 . DNA Database of Japan (DDBJ) 3. Prosite 2. Sequence Retrieval System (SRS) 3. These macromolecules have a fixed structure. Protein Information Resource (PIR) Secondary Database 1. Class. Protein Family (PFAM) Nucleotide Sequence Database 1.
phylogeneticclassification and references to published literature. In addition to sequence data.400. EMBL: The EMBL Nucleotide Sequence Database is a comprehensive database of DNA andRNA sequences collected from the scientific literature and patent applications anddirectly submitted from researchers and sequencing groups. PROSITE: The PROSITE dictionary of sites and patterns in proteins prepared by Amos Bairoch atthe University of Geneva. Catalytic activity. SwissProt: This is a protein sequence database that provides a high level of integration with other databases and also has a very low level of redundancy (means less identical sequences are present in the database).615 sequence entries. Data collection isdone in collaboration with GenBank USA) and the DNA Database of Japan (DDBJ).The database currently doubles in size every 18 months and currently (June 1994) contains nearly 2 million bases from 182.000 bases and 183. It has a flat file structure that is an ASCII text file.There areapproximately 191. GenBank filescontain information like accession numbers and gene names. EC-ENZYME: The 'ENZYME' data bank contains the following data for each type of characterized enzyme for which an EC number has been provided: EC number. recommended name. Alternative names. Cofactors. readableby both humans and computers.Bioinformatics 16 Genbank: GenBank (Genetic Sequence Databank) is one of the fastest growing repositories of known genetic sequences. Pointers to the SWISS-PROT entree(s) that correspond to the 16 .000 sequences as of June 1994.
Antonarakis at John Hopkins University.00:March 31. and professional and scientific education by providing for the storage and dissemination of data about genes and other DNA markers. It is the most comprehensive and expertly annotated protein sequence database. GDB: The GDB Human Genome Data Base supports biomedical research. Francomano and Stylianos E. distributing magnetic tapes. It is operated by Rutgers. and bibliographic information. The PIR serves the scientific community through on-line access. The State University of New Jersey and the San Diego Super computer Center at the University of California. and Cryo-EM. 1994 67. PIR-PSD: PIR (Protein Information Resource) produces and distributes the PIRInternational Protein Sequence Database (PSD).Bioinformatics enzyme. San Diego.423 entries 17 . NMR. clinical medicine. Release 40. and performing off-line sequence identification services for researchers. 17 RCSB-PDB : The RCSB PDB contains 3-D biological macromolecular structure data from X-ray crystallography. genetic disease and locus information. Pointers to disease(s) associated with a deficiency of the enzyme. OMIM: The Mendelian Inheritance in Man data bank (MIM) is prepared by Victor Mc Kusickwiththe assistance of Claire A. map location.
can be obtained via ftp. Human Chromosome X. This initial release contains the following kinds of information: Loci (over15.000 references). the C. The software. 3500 loci from 40 mammalian species).000 current and withdrawn symbols). elegans genome project (funded by theMRC and NIH). for example neuromuscular tissues. ACeDB databases are available for the following species: C. Homologies (1300 mouse loci. Secondary databases (like Prosite) contain the information derived from protein sequences. GENETIC MAP: production of micro-satellite probes and the localization of chromosomes. PIR and Swiss Prot are primary databases that contain protein sequences as 'raw' data. MGD: The Mouse Genome Databases: MGD is a comprehensive database of genetic information on the laboratory mouse. ACeDB (A Caenorhabditis elegans Database): Containing data from the Caenorhabditis Genetics Center (funded by the NIH National Center for Research Resources). secondary and composite depending upon the content stored in them. Experimental data (from 2400 published articles). as well as the C.000).297 residues. Primary databases are combined and filtered to form non-redundant composite database Genethon Genome Databases: PHYSICAL MAP: computation of the human genetic map using DNA fragments in the form of YAC contigs. 18 . elegans data. Probes and Clones (about 10. GENEXPRESS (cDNA): catalogue the transcripts required for protein synthesis obtained from specific tissues. and the worm community. HumanChromosome 21. elegans. PCR primers (currently 500primer pairs). to create a genetic map to aid in the study of hereditary diseases. Protein sequence databases are classified as primary. ACeDB is also the name of the generic genome database software in use by an increasing number of genome projects.Bioinformatics 18 19. Drosophila melanogaster. mycobacteria.747. Bibliography (over 18.
andSorghum bicolor. Schizosaccharomyces pombe. by hand. maize.Bioinformatics 19 Arabidopsis. grains. dentistry. The evolution of computing power and storage capacity has. so far. Gossypium hirsutum. Not only can computers be used to store and organize sequence information into databases. Saccharomyces cerevisiae. MEDLINE contains all citations published in Index Medicus. forest trees. Journal articles are indexed for MEDLINE. using NLM's controlled vocabulary. all necessary sequence information of interest to a given project from published journal articles quickly became a formidable task. soybeans. and the preclinical sciences. been able to outpace the increase in sequence information being created. It could take weeks to months for a researcher to search sequences by hand in order to find related genes or proteins. Aspergillus nidulans. rice. but they can also be used to analyze sequence data rapidly. Bos taurus. After collection. MeSH (Medical Subject Headings). the organization and analysis of this data still remained. Neurosporacrassa. MEDLINE: MEDLINE is NLM's premier bibliographic database covering the fields of medicine. Citations include the English abstract when published with the article (approximately 70% of the current file). and corresponds in part to the International Nursing Index and the Index to Dental Literature. For researchers to benefit from all this information. Theoretical scientists have derived new and 19 . two additional things were required: 1) Ready access to the collected pool of sequence information and 2) A way to extract from this pool only those sequences of interest to a given researcher Simply collecting. and their citations are searchable. Computer technology has provided the obvious solutionto this problem. nursing.Solanaceae. veterinary medicine. however.
These comparisons become the basis for determining gene function. has evolved and expanded so that nearly everyone has access to this information and the tools necessary to analyze it. homology. This web of connections. a sequence alignment is a way of arranging the primary sequences of DNA. developing phylogenetic relationships and simulating protein models. or protein to identify regions of similarity that may be a con sequence of functional. Sequence Analysis: In bioinformatics. Aligned sequences of nucleotide oramino acid residues are typically represented as rows within a matrix. RNA. structural. The property of sharing a common ancestor. or evolutionary relationships between the sequences. can be a very powerful indicator in bioinformatics. now known as the Internet. Gaps are inserted between the residues so that residues with identical or similar characters are aligned in successive columns. The physical linking of a vast array of computers in the 1970's provided a few biologists with ready access to the expanding pool of sequence information. Databases of existing sequencing data can be used to identify homologues of new molecules that have been amplifie and sequenced in the lab. 20 .Bioinformatics 20 sophisticated algorithms which allow sequences to be readily compared using probability theories.
Sequence alignment canbe used for non-biological sequences. mismatches can be interpreted as point mutations and gaps as indels (that is. the degree of similarity between amino acids occupying a particular position in the sequence can be interpreted as a rough measure of how conserved a particular region or sequence motif is among lineages.Bioinformatics 21 A sequence alignment. The absence of substitutions. the substitution of amino acids whose side chains have similar biochemical properties) in a particular region of the sequence. Although DNA and RNA nucleotide bases are more similar to each other than to amino acids. the conservation of base pairing can dictate a similar functional or structural role. 21 . or the presence of only very conservative substitutions (that is. such as those present in natural language or in financial data. If two sequences in an alignment share a common an cestor. produced by ClustalW between two human zinc finger proteins identified by GenBank accession number. suggest that this region has structural or functional importance. insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. In protein sequence alignment.
many of which were originally developed in conjunction with a specific alignment program or implementation. Calculating a global alignment is a form of global optimization that "forces" the alignment to span the entire length of all query sequences. global alignments 2. the use of specific tools authored by individual research laboratories can be complicated by limited file format compatibility. Sequence alignments can be stored in a wide variety of text-based file formats.) A general global alignment technique is called the 22 . Illustration of global and local alignments demonstrating the 'gappy' quality of global alignments that can occur if sequences are insufficiently similar Global alignments. Most web-based tools allow a number of input and output formats. A general conversion program is available at DNA Baser or Readseq (for Readseq you must upload your files on a foreign server and provide your email address). (This does not mean global alignments cannot end in gaps. such as FASTA format and Gen Bank format.Bioinformatics 22 Computational approaches to sequence alignment generally fall into two categories: 1. By contrast. which attempt to align every residue in every sequence. local alignments. including slow but formally optimizing methods like dynamic programming and efficient heuristic or probabilistic methods designed for large-scale database search. but can be more difficult to calculate because of the additional challenge of identifying the regions of similarity. local alignments identify regions of similarity within long sequences that are often widely divergent overall. however. are most useful when the sequences in the query set are similar and of roughly equal size. A variety of computational algorithms have been applied to the sequence alignment problem. Local alignments are often preferable.
The three primary methods of producing pair wise alignments are dot-matrix methods. The Smith-Waterman algorithm is a general local alignment method also based on dynamic programming. Longer MUM sequences typically reflect closer relatedness. With sufficiently similar sequences.Bioinformatics Needleman-Wun sch algorithm and is based on dynamic programming. Pairwise alignment : Pair wise sequence alignment methods are used to find the bestmatching piecewise(local) or global alignments of two querysequences. all three pair wise methods have difficulty with highly repetitive sequences of low information content . multiple sequence alignment techniques can also align pairs of sequences. Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs 23 within their larger sequence context.especially where the number of repetitions differ in the two sequences to be aligned. Pair wise alignments can only be used between two sequences at a time. Although each method has its individual strengths and weaknesses. or the longest subsequence that occurs in both query sequence. and word methods . there is no Difference between local and global alignments. dynamic programming. Multiple sequence alignment: 23 . however. One way of quantifying the utility of a given pairwise alignment is the 'maximum unique match'. but they are efficient to calculate and are often used for methods that do not require extreme precision (such as searching a database for sequences with high homology to a query).
• The Bioinformatics Tools may be categorized into following categories: • • • Homology and Similarity Tools Protein Function Analysis Structural Analysis 24 . Factors that must be taken into consideration when designing these tools are: • The end user (the biologist) may not be a frequent user of computer technology and thus it should be very user friendly. retrieving and analysis of Biological data and extracting the information from them.Bioinformatics Multiple sequence alignment is an extension of pair wise alignment to incorporate more than two sequences at a time. Multiple alignment methods try to align all of the sequences in a given query set. Multiple alignments are often used in identifying conserved sequence regions across a group of sequences hypothesized to be evolutionarily related. Alignments are also used to aid in establishing evolutionary relationships by constructing phylogenetic trees. Multiple sequence alignments are computationally difficult to produce and most formulations of the problem lead to NP-complete combinatorial optimization problems. BioInformatics Tools The Bioinformatics tools are the software programs for the saving. Such conserved sequence motifs can be used in conjunction with 24 structural and mechanistic information to locate the catalytic active sites of enzymes. These software tools must be made available over the internet given the global distribution of the scientific research community. Nevertheless. the utility of these alignments in bioinformatics has led to the development of a variety of methods suitable for aligning three or more sequences.
Bioinformatics • 25 Sequence Analysis Homology and Similarity Tools The term homology implies a common evolutionary relationship between two traits -whether they are DNA sequences or bristle patterns on a fly's nose. identification of mutations. more detailed analysis on your query sequence including evolutionary analysis. This group of programs allow you to compare your protein sequence to the secondary (or derived) protein databases that contain information on motifs. Sequence Analysis This set of tools allows you to carry out further. The function of a protein is more directly a consequence of its structure rather than its sequence with structural homologs tending to share functions. The determination of a protein's 2D/3D structure is crucial in the study of its function. Protein Function Analysis Function Analysis is Identification and mapping of all functional elements (both coding and non-coding) in a genome. Highly significant hits against these different pattern databases allow you to approximate the biochemical function of your query protein. hydropathy regions. The identification of these and other biological properties are all clues that aid the search to elucidate the specific function of your sequence. This set of tools can be used to identify similarities between novel query sequences of unknown structure and function and database sequences whose structure and function have been elucidated. 25 . signatures and protein domains. Homologous sequences are sequences that are related by divergence from a common ancestor. Structural Analysis This set of tools allow you to compare structures with the known structure databases. CpG islands and compositional biases. Thus the degree of similarity between two sequences can be measured while their homology is a case of being either true of false.
immunoglobulins. It was the first widely used algorithm for database similarity searching. the scores of segments in which there are multiple word hits are calculated ("init1"). Initially. similarities and differences can be seen. Later the scores of several segments may be summed to generate an "initn" score. protein motif identification and domain analysis. and tentative human consensus sequences. and much more. FASTA A database search tool used to compare a nucleotide or peptide sequence to a sequence database. malaria. Specialized BLASTs are also available for human. microbial.Bioinformatics Bioinformatics Tools 26 BLAST: The Basic Local Alignment Search Tool (BLAST) for comparing gene and protein sequences against others in public databases. and lines them up so that the identities. calculates the best match for the selected sequences. free open source software analysis package specially developed for the needs of the molecular biology user community. Within EMBOSS you will find around 100 programs (applications) for sequence alignment. EMBOSS EMBOSS (The European Molecular Biology Open Software Suite) is a new. as well as for vector contamination. and BLAST 2 sequences. database searching with sequence patterns. Clustalw ClustalW is a general purpose multiple sequence alignment program for DNA or proteins. The program looks for optimal local alignments by scanning the sequence for small matches called "words". nucleotide sequence pattern analysis. The program is based on the rapid sequence algorithm described by Lipman and Pearson. 26 . It produces biologically meaningful multiple sequence alignments of divergent sequences. now comes in several types including PSI-BLAST. codon usage analysis for small genomes. and other genomes. An optimized alignment that includes gaps is shown in the output as "opt". PHI-BLAST. The sensitivity and speed of the search are inversely related and controlled by the "k-tup" variable which specifies the size of a "word".
Bioinformatics RasMol It is a powerful research tool to display the structure of DNA. In Bioinfomatics knowledge of many branches are required like biology. Protein Explorer. APPLICATIONS OF BIOINFORMATICS Bioinformatics is the use of IT in biotechnology for the data storage. laws of physics & chemistry. proteins. Physiome Sciences' computer-based biological simulation technologies and Bioinformatics Solutions' PatternHunter are two examples of the growing adoption of Java in bioinformatics. One example of perl project is BioPerl project. Perl in Bioinformatics: Perl is also being used in the processing of biological data. and of course sound knowledge of IT to analyze biotech data. and smaller molecules. Application Programs 27 JAVA in Bioinformatics: Due to Platform independence nature of Java. it is emerging as a key player in bioinformatics. data warehousing and analyzing the DNA sequences. computer science. Bioinformatics is not limited to 27 . mathematics. is an easier to use program. a derivative of RasMol.
It is the comprehensive application of mathematics (e.. but in reality it can be used to solve many biological problems and find out how living things works. science (e. These include the fallowing: Molecular medicine More drug targets Personalised medicine Preventive medicine Gene therapy Microbial genome applications Waste cleanup Climate change Alternative energy sources Biotechnology Antibiotic resistance Forensic analysis of microbes The reality of bioweapon creation Evolutuionary studies Agriculture Crops Insect resistance Improve nutritional quality Grow crops in proper soils and that are drought resistant Animals Comparative studies 28 . and a core set of problem-solving methods (e.g. The science of bioinformatics has many beneficial uses in the modern day world.g.Bioinformatics 28 the computing data...g. computer algorithms) to the understanding of living systems. probability and statistics). biochemistry).
Bioinformatics • 29 Major Application : Designing Drugs Understanding How Structures Bind Other Molecules (Function) Designing Inhibitors Docking.g. how many kinases in Yeast 29 . Structure Modeling • Major Application II: Finding Homologs Major Application I|I: Overall Genome Characterization Overall Occurrence of a Certain Feature in the Genome e.
Identification of nucleotide sequences of functional genes. tissues and organs. Prediction of functional gene products. Proteins).D structure of proteins. Development of models for the functioning various cells. 30 .Bioinformatics 30 Compare Organisms and Tissues Expression levels in Cancerous vs Normal Tissues Sequence mapping of bimolecules (DNA. Molecular modeling of bimolecules. Designing of drugs for medical treatment. RNA. For the prediction of 3. To trace the evolutionary tree of genes. Handling of vast biological data which otherwise is not possible. Finding of sites that can be cut by restriction enzymes.
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