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Bio in for Ma Tics

Bio in for Ma Tics

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Published by: Samudrala Vijaykumar on Oct 07, 2011
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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."

From Webopedia:
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 .

Biological Science and computational Science. Here is the data of historical events for both biology and computer sciences. He did experiment on the crossfertilization of different colors of the same species.C. He carefully recorded the data and analyzed the data.Bioinformatics 5 . Mendel in 1865. is known as the "Father of Genetics". This was the start of Bioinformatics history. and before the discovery of genetic inheritance by G. Gregor Mendel. History of Bioinformatics The Modern bioinformatics is can be classified into two broad categories. B. The history of biology in general. is extremely sketch and inaccurate. Mendel illustrated that the 5 .

comparing their microscopic structure to that of the living organisms they resembled.600 kinds of plants. John Ray. The advancement of computing in 1960-70s resulted in the basic methodology of bioinformatics. two important things happened in the field of genomics. Sweden. 7. Uppsala University. In 1972. The understanding of genetics has advanced remarkably in the last thirty years. IV. Stanley Cohen. was coined. Richard Owen elaborated the distinction of homology andanalogy. He also described microscopic examinations of fossilized plants and animals. "The moving-boundary method of studying the electrophoresis of proteins" (published in Nova Acta Regiae Societatis Scientiarum Upsaliensis. The chromosome theory of heredity is proposed by Sutton and Boveri. A new technique. Tiselius. Morgan). First ever linkage map created by Columbia undergraduate Alfred Sturtevant (working with T. it is the 1990s when the INTERNET arrived when the full fledged bioinformatics field was born. Ernst Haeckel (Häckel) outlined the essential elements of modern zoological classification. established the theory of genetic inheritance. "bioinformatics". is introduced by Tiselius for separating proteins in solution. as shown by Lederberg and Tatum. His book gave the first definition of species based upon common descent. In that same year. In 1973. John Ray's in his book "Historia Plantarum" catalogued and described 18. Gregory Mendel (1823-1884). Vol. and suggested a plausible mechanism for their formation. He argued for an organic origin of fossils. Antoni van Leeuwenhoek discovered bacteria. No. However. 1665 1683 1686 1843 1864 1865 1902 1962 1905 1913 1930 1946 6 . BioInformatics Events Robert Hooke published Micrographia. Annie Chang and Herbert Boyer produced the first recombinant DNA organism.H. described the cellular structure of cork. The events listed in the list occurred long before the term. Pauling's theory of molecular evolution The word "genetics" is coined by William Bateson. Here are some of the major events in bioinformatics over the last several decades. Ser. electrophoresis. working independently. 4) Genetic material can be transferred laterally between bacterial cells. Austria.Bioinformatics inheritance of traits could be more easily explained if it was controlled by factors passed down from generation to generation. Paul berg made the first recombinant DNA 6 molecule using ligase.

PubMed The genome for Pseudomonas aeruginosa (6. The human genome (3 Giga base pairs) is published. Sidney Brenner. Hinxton. thaliana genome (100 Mb) is secquenced. Matthew Meselson. The large-scale organization of metabolic networks.Bioinformatics 1952 1961 1965 1970 1977 7 Alfred Day Hershey and Martha Chase proved that the DNA alone carries genetic information. 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.3 Mbp) is published. Tombor B. UK EMBL European Bioinformatics Institute. identify messenger RNA. The A. Oltvai ZN. This was proved on the basis of their bacteriophage research. François Jacob. Hinxton. Barabasi AL. Nature 2000 Oct 5. UK First bacterial genomes completely sequenced Yeast genome completely sequenced PSI-BLAST Worm (multicellular) genome completely sequenced Fly genome completely sequenced Jeong H.407(6804):651-4. Albert R. 7 .

or visualize such data. Computational Biology: The development and application of data analytical and theoretical methods. archive.structure and function.behavioral or health data.of course possible to compare genomics by comparing more or less representative subsets of genes within genomes. Pharmacogenomics: It is the application of genomic approaches and technologies to the identification of drug targets. Genomics: Genomics is any attempt to analyze or compare the entire genetic complement of a species . pharmacogenomics is using genetic information to predict whether a drug will help make a patient well or sick. retrieval and analysis of chemical information from data to chemical knowledge. 8 .( or) application of computational tools and approaches for expanding the use of biological.Bioinformatics 8 DEFINITIONS RELATED TO BIOINFORMATICS : Bioinformatics: Research. medical.It is . including those to acquire store. behavioral. Pharmacogenetics: It is the study of how the actions of and reactions to drugs vary with the patients genes. and social systems. Proteomics: It is the study of proteins-their location. Chemical informatics: Computer assisted storage.In short. development. organize. mathematical modelling and computational simulation techniques to the study of biological. analyze.

it is of interest to compare it with previously characterised sequences.coli. AIMS OF BIOINFORMATICS : The aims of bioinformatics include:  First. the Protein Data Bank for 3D macromolecular structures. For example. 9 . e.g. the fruit fly and the bacterium E. While data-curation is an essential task. 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. having sequenced a particular protein. Thus the purpose of bioinformatics extends much further. Development of such resources dictates expertise in computational theory as well as a thorough under-standing of biology.  The second aim is to develop tools and resources that aid i n the analysis of data. 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. Biophysics: An interdisciplinary field which applies techniques from the physical sciences to understanding biological structure and function.Bioinformatics 9 Comparative genomics: The study of human genetics by comparisons with model organisms such as mice. Pharmacoinformatics: It concentrates on the aspects of bioinformatics dealing with drug discovery. the information stored in these databases is essentially use-less until analysed.

 To facilitate usage of the database and analytical software available to the scientific community.genetics and biochemistry. Traditionally. 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. 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. biological studies examined individual systems in detail and frequently compared them with a few that are related.  To coordinate worldwide efforts to gather biological data 10 . 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. In bioinformatics.Bioinformatics 10  The third aim is to use these tools to analyse the data and interpret the results in a biologically meaningful manner. National centre for Biotechnology Information (NCBI) In November 1988. 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.

PROT database dbEST&dbSTS PDB NDB 11 . dbEST European Bioinformatics institute(EBI): EBI is an outstation of the European molecular biology laboratory(EMBL) located at Hinxton. Databases at EBI:      EMBL database SWISS.g:PIR’s complete database which consists of PIR!+PIR2+PIR3. Redundant nucleotide sequence databases-Eg. redundant protein sequence databases –E.  Nucleotide sequence: These are DNA and RNA sequences derived from less automated sequencing projects I. England. 11 Databases supported by NCBI:  Protein sequence: These are experimentally sequenced proteins and translated nucleotide sequences from nucleotide libraries.Bioinformatics  To conduct research in computerised analysis of structure function relationships for key biological molecules. 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. 1.

Perl or Python. Learn to use sequence analysis and molecular modeling software. Java and HTML should be known by Bioinformatician. 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. This platform. 1. Molecular Biology 2.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. Computer Programming Language like C/C++. 7. FASTA etc. 6. Experience with one or more of Molecular Biology software packages. Here is the important topics very essential to enter in this profession. Database Management Systems Learn Oracle and MySQL (Free Database Server) which is extensively used for store gigabytes of biotech data for further analysis. Some of the molecular biology packages are GCG. Central Dogma of molecular biology 3. BLAST. BIOLOGICAL DATABASES : 12 . its very important to learn these operating system. 4.

literature citations associated with the sequence. and. A simple database might be a single file containing many records. query. often.Easy access to the information. and retrieve components of the data stored within the system. the scientific name of the source organism from which it waisolated. each of which includes the same set of information.Bioinformatics 13 A biological database is alarge . For example. For researchers to benefit from the data stored in a database. and 13 . the input sequence with description of the type of molecule. a record associated with a nucleotide sequence database typically contains information such as contact name. two additional requirements must be met: 1.organized body of persistent data usually associated with computerized software designed to update.

a lot of bioinformatics work is concerned with thetechnology of databases. RNA and DNA are the proteins that store the 14 .Bioinformatics 2.A method for extracting only that information needed to answer a specific biological question. 14 Currently. 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. 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.

Nuclear Receptor Database (NucleaRDB) 5. which can be analyzed by biologists with the help of bioinformatics tools and databases. Swiss-Prot 2. Prosite 2. Topology and Homologous super family Protein Sequence Database • Primary Database 1. Class. Architecture. G-Protein Coupled Receptor Database (GPCRDB) 4. Restriction Enzyme Database (REBASE) 3. Literature Database – PubMed 15 . GenBank 2. Catalogue of Databases (DBCAT) Other Databases 1. Structural Classification of Proteins 3. DNA Database of Japan (DDBJ) 3. National Center for Biotechnology Information (NCBI) 2. Protein Data Bank (PDB) 2. Sequence Retrieval System (SRS) 3. Receptor-Ligand Database (ReliBase) 2. Protein Structure Database: 1. European Molecular Biology Laboratory (EMBL) Composite Databases 1.Bioinformatics 15 hereditary information about an organism. Protein Information Resource (PIR) Secondary Database 1. These macromolecules have a fixed structure. Protein Family (PFAM) Nucleotide Sequence Database 1.

Alternative names.Bioinformatics 16 Genbank: GenBank (Genetic Sequence Databank) is one of the fastest growing repositories of known genetic sequences. phylogeneticclassification and references to published literature. Catalytic activity. recommended name.000 bases and 183. In addition to sequence data. 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. It has a flat file structure that is an ASCII text file. GenBank filescontain information like accession numbers and gene names.400. readableby both humans and computers.000 sequences as of June 1994. PROSITE: The PROSITE dictionary of sites and patterns in proteins prepared by Amos Bairoch atthe University of Geneva.There areapproximately 191. 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. 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).The database currently doubles in size every 18 months and currently (June 1994) contains nearly 2 million bases from 182. Cofactors.615 sequence entries. Data collection isdone in collaboration with GenBank USA) and the DNA Database of Japan (DDBJ). Pointers to the SWISS-PROT entree(s) that correspond to the 16 .

OMIM: The Mendelian Inheritance in Man data bank (MIM) is prepared by Victor Mc Kusickwiththe assistance of Claire A.00:March 31. PIR-PSD: PIR (Protein Information Resource) produces and distributes the PIRInternational Protein Sequence Database (PSD). GDB: The GDB Human Genome Data Base supports biomedical research. and performing off-line sequence identification services for researchers. and Cryo-EM. It is the most comprehensive and expertly annotated protein sequence database.Bioinformatics enzyme. Francomano and Stylianos E. San Diego. NMR. 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.423 entries 17 . map location. It is operated by Rutgers. distributing magnetic tapes. clinical medicine. and bibliographic information. and professional and scientific education by providing for the storage and dissemination of data about genes and other DNA markers. 17 RCSB-PDB : The RCSB PDB contains 3-D biological macromolecular structure data from X-ray crystallography. 1994 67. Release 40. Pointers to disease(s) associated with a deficiency of the enzyme. Antonarakis at John Hopkins University. genetic disease and locus information.

GENETIC MAP: production of micro-satellite probes and the localization of chromosomes. Human Chromosome X. secondary and composite depending upon the content stored in them. Drosophila melanogaster.000 references). 18 . This initial release contains the following kinds of information: Loci (over15.297 residues. as well as the C. ACeDB databases are available for the following species: C. Homologies (1300 mouse loci.000). MGD: The Mouse Genome Databases: MGD is a comprehensive database of genetic information on the laboratory mouse. mycobacteria. can be obtained via ftp.Bioinformatics 18 19. to create a genetic map to aid in the study of hereditary diseases. ACeDB is also the name of the generic genome database software in use by an increasing number of genome projects. Bibliography (over 18. Secondary databases (like Prosite) contain the information derived from protein sequences. PIR and Swiss Prot are primary databases that contain protein sequences as 'raw' data. elegans data. elegans. Protein sequence databases are classified as primary. PCR primers (currently 500primer pairs). the C. 3500 loci from 40 mammalian species). Probes and Clones (about 10. Experimental data (from 2400 published articles).000 current and withdrawn symbols). elegans genome project (funded by theMRC and NIH). ACeDB (A Caenorhabditis elegans Database): Containing data from the Caenorhabditis Genetics Center (funded by the NIH National Center for Research Resources). 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. and the worm community. HumanChromosome 21.747. The software. GENEXPRESS (cDNA): catalogue the transcripts required for protein synthesis obtained from specific tissues. for example neuromuscular tissues.

Journal articles are indexed for MEDLINE. and corresponds in part to the International Nursing Index and the Index to Dental Literature. For researchers to benefit from all this information. Schizosaccharomyces pombe. Bos taurus. and their citations are searchable. maize. Theoretical scientists have derived new and 19 . rice. been able to outpace the increase in sequence information being created. forest trees.Solanaceae. soybeans. Neurosporacrassa. It could take weeks to months for a researcher to search sequences by hand in order to find related genes or proteins. however. Aspergillus nidulans.Bioinformatics 19 Arabidopsis. so far. all necessary sequence information of interest to a given project from published journal articles quickly became a formidable task. the organization and analysis of this data still remained. dentistry. MeSH (Medical Subject Headings). veterinary medicine. and the preclinical sciences. 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. nursing. After collection. MEDLINE: MEDLINE is NLM's premier bibliographic database covering the fields of medicine. MEDLINE contains all citations published in Index Medicus. but they can also be used to analyze sequence data rapidly. Computer technology has provided the obvious solutionto this problem. Gossypium hirsutum. Saccharomyces cerevisiae. grains. by hand. Citations include the English abstract when published with the article (approximately 70% of the current file). Not only can computers be used to store and organize sequence information into databases. The evolution of computing power and storage capacity has. using NLM's controlled vocabulary. andSorghum bicolor.

This web of connections. Databases of existing sequencing data can be used to identify homologues of new molecules that have been amplifie and sequenced in the lab. or evolutionary relationships between the sequences. 20 . can be a very powerful indicator in bioinformatics. Aligned sequences of nucleotide oramino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that residues with identical or similar characters are aligned in successive columns.Bioinformatics 20 sophisticated algorithms which allow sequences to be readily compared using probability theories. These comparisons become the basis for determining gene function. The property of sharing a common ancestor. has evolved and expanded so that nearly everyone has access to this information and the tools necessary to analyze it. 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. now known as the Internet. Sequence Analysis: In bioinformatics. structural. RNA. or protein to identify regions of similarity that may be a con sequence of functional. a sequence alignment is a way of arranging the primary sequences of DNA. homology. developing phylogenetic relationships and simulating protein models.

Bioinformatics 21 A sequence alignment. such as those present in natural language or in financial data. suggest that this region has structural or functional importance. Sequence alignment canbe used for non-biological sequences. The absence of substitutions. or the presence of only very conservative substitutions (that is. mismatches can be interpreted as point mutations and gaps as indels (that is. Although DNA and RNA nucleotide bases are more similar to each other than to amino acids. insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. the conservation of base pairing can dictate a similar functional or structural role. 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. 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. the substitution of amino acids whose side chains have similar biochemical properties) in a particular region of the sequence. 21 . In protein sequence alignment.

Bioinformatics 22 Computational approaches to sequence alignment generally fall into two categories: 1. such as FASTA format and Gen Bank format. which attempt to align every residue in every sequence. 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). Illustration of global and local alignments demonstrating the 'gappy' quality of global alignments that can occur if sequences are insufficiently similar Global alignments. local alignments identify regions of similarity within long sequences that are often widely divergent overall. Sequence alignments can be stored in a wide variety of text-based file formats. the use of specific tools authored by individual research laboratories can be complicated by limited file format compatibility. but can be more difficult to calculate because of the additional challenge of identifying the regions of similarity. local alignments. Local alignments are often preferable. Most web-based tools allow a number of input and output formats. including slow but formally optimizing methods like dynamic programming and efficient heuristic or probabilistic methods designed for large-scale database search. 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. 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. global alignments 2. (This does not mean global alignments cannot end in gaps. however.) A general global alignment technique is called the 22 . By contrast.

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). dynamic programming. The Smith-Waterman algorithm is a general local alignment method also based on dynamic programming. With sufficiently similar sequences. Longer MUM sequences typically reflect closer relatedness. 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. Multiple sequence alignment: 23 . 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. there is no Difference between local and global alignments.Bioinformatics Needleman-Wun sch algorithm and is based on dynamic programming. One way of quantifying the utility of a given pairwise alignment is the 'maximum unique match'.especially where the number of repetitions differ in the two sequences to be aligned. however. or the longest subsequence that occurs in both query sequence. Although each method has its individual strengths and weaknesses. and word methods . Pairwise alignment : Pair wise sequence alignment methods are used to find the bestmatching piecewise(local) or global alignments of two querysequences. The three primary methods of producing pair wise alignments are dot-matrix methods. Pair wise alignments can only be used between two sequences at a time.

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. Such conserved sequence motifs can be used in conjunction with 24 structural and mechanistic information to locate the catalytic active sites of enzymes. 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. • The Bioinformatics Tools may be categorized into following categories: • • • Homology and Similarity Tools Protein Function Analysis Structural Analysis 24 . These software tools must be made available over the internet given the global distribution of the scientific research community.Bioinformatics Multiple sequence alignment is an extension of pair wise alignment to incorporate more than two sequences at a time. Multiple alignments are often used in identifying conserved sequence regions across a group of sequences hypothesized to be evolutionarily related. BioInformatics Tools The Bioinformatics tools are the software programs for the saving. the utility of these alignments in bioinformatics has led to the development of a variety of methods suitable for aligning three or more sequences. Multiple alignment methods try to align all of the sequences in a given query set. Nevertheless.

identification of mutations. This group of programs allow you to compare your protein sequence to the secondary (or derived) protein databases that contain information on motifs. Structural Analysis This set of tools allow you to compare structures with the known structure databases.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. hydropathy regions. Sequence Analysis This set of tools allows you to carry out further. The identification of these and other biological properties are all clues that aid the search to elucidate the specific function of your sequence. 25 . Homologous sequences are sequences that are related by divergence from a common ancestor. The determination of a protein's 2D/3D structure is crucial in the study of its function. CpG islands and compositional biases. The function of a protein is more directly a consequence of its structure rather than its sequence with structural homologs tending to share functions. 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. more detailed analysis on your query sequence including evolutionary analysis. Protein Function Analysis Function Analysis is Identification and mapping of all functional elements (both coding and non-coding) in a genome. signatures and protein domains. Highly significant hits against these different pattern databases allow you to approximate the biochemical function of your query protein. Thus the degree of similarity between two sequences can be measured while their homology is a case of being either true of false.

and tentative human consensus sequences. microbial. Initially. Within EMBOSS you will find around 100 programs (applications) for sequence alignment. PHI-BLAST. The program looks for optimal local alignments by scanning the sequence for small matches called "words". FASTA A database search tool used to compare a nucleotide or peptide sequence to a sequence database. the scores of segments in which there are multiple word hits are calculated ("init1"). codon usage analysis for small genomes. 26 . It was the first widely used algorithm for database similarity searching. now comes in several types including PSI-BLAST. nucleotide sequence pattern analysis. as well as for vector contamination. The program is based on the rapid sequence algorithm described by Lipman and Pearson. and other genomes. and BLAST 2 sequences. similarities and differences can be seen. protein motif identification and domain analysis. Clustalw ClustalW is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. and much more. EMBOSS EMBOSS (The European Molecular Biology Open Software Suite) is a new. database searching with sequence patterns. malaria. An optimized alignment that includes gaps is shown in the output as "opt". calculates the best match for the selected sequences. Specialized BLASTs are also available for human. 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 Bioinformatics Tools 26 BLAST: The Basic Local Alignment Search Tool (BLAST) for comparing gene and protein sequences against others in public databases. free open source software analysis package specially developed for the needs of the molecular biology user community. immunoglobulins. and lines them up so that the identities. Later the scores of several segments may be summed to generate an "initn" score.

and smaller molecules. and of course sound knowledge of IT to analyze biotech data.Bioinformatics RasMol It is a powerful research tool to display the structure of DNA. One example of perl project is BioPerl project. Protein Explorer. it is emerging as a key player in bioinformatics. is an easier to use program. In Bioinfomatics knowledge of many branches are required like biology. data warehousing and analyzing the DNA sequences. APPLICATIONS OF BIOINFORMATICS Bioinformatics is the use of IT in biotechnology for the data storage. Physiome Sciences' computer-based biological simulation technologies and Bioinformatics Solutions' PatternHunter are two examples of the growing adoption of Java in bioinformatics. mathematics. a derivative of RasMol. Perl in Bioinformatics: Perl is also being used in the processing of biological data. Application Programs 27 JAVA in Bioinformatics: Due to Platform independence nature of Java. Bioinformatics is not limited to 27 . laws of physics & chemistry. computer science. proteins.

biochemistry).. and a core set of problem-solving methods (e.g. science (e.g.Bioinformatics 28 the computing data.. It is the comprehensive application of mathematics (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 . probability and statistics)..g. The science of bioinformatics has many beneficial uses in the modern day world. but in reality it can be used to solve many biological problems and find out how living things works. computer algorithms) to the understanding of living systems.

g.Bioinformatics • 29 Major Application : Designing Drugs  Understanding How Structures Bind Other Molecules (Function)  Designing Inhibitors  Docking. Structure Modeling • Major Application II: Finding Homologs Major Application I|I: Overall Genome Characterization  Overall Occurrence of a Certain Feature in the Genome e. how many kinases in Yeast 29 .

D structure of proteins. 30 .  Finding of sites that can be cut by restriction enzymes.  Development of models for the functioning various cells.  Identification of nucleotide sequences of functional genes. tissues and organs.  Prediction of functional gene products.  Handling of vast biological data which otherwise is not possible.  Molecular modeling of bimolecules.  For the prediction of 3.  To trace the evolutionary tree of genes.  Designing of drugs for medical treatment.Bioinformatics 30  Compare Organisms and Tissues Expression levels in Cancerous vs Normal Tissues  Sequence mapping of bimolecules (DNA. Proteins). RNA.

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