Bioinformatics

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Introduction

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

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Bioinformatics

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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:
"Bioinformatics

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.

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Bioinformatics

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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.

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Bioinformatics 4 4 .

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

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

The human genome (3 Giga base pairs) is published. 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 large-scale organization of metabolic networks. The A. thaliana genome (100 Mb) is secquenced.3 Mbp) is published. François Jacob. Oltvai ZN. PubMed The genome for Pseudomonas aeruginosa (6. Barabasi AL. Sidney Brenner. UK First bacterial genomes completely sequenced Yeast genome completely sequenced PSI-BLAST Worm (multicellular) genome completely sequenced Fly genome completely sequenced Jeong H. identify messenger RNA. Matthew Meselson. Hinxton. Tombor B. Albert R. Nature 2000 Oct 5.407(6804):651-4.Bioinformatics 1952 1961 1965 1970 1977 7 Alfred Day Hershey and Martha Chase proved that the DNA alone carries genetic information. Hinxton. This was proved on the basis of their bacteriophage research. 7 . UK EMBL European Bioinformatics Institute.

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

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

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. Traditionally. In bioinformatics.  To facilitate usage of the database and analytical software available to the scientific community.genetics and biochemistry. 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.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. biological studies examined individual systems in detail and frequently compared them with a few that are related. 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. National centre for Biotechnology Information (NCBI) In November 1988.  To coordinate worldwide efforts to gather biological data 10 .

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

This platform. Perl or Python.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. Java and HTML should be known by Bioinformatician. BIOLOGICAL DATABASES : 12 . Central Dogma of molecular biology 3. Molecular Biology 2. 6. 4. Learn to use sequence analysis and molecular modeling software. FASTA etc. 7. Computer Programming Language like C/C++. 1. 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. Experience with one or more of Molecular Biology software packages. 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. its very important to learn these operating system. Here is the important topics very essential to enter in this profession. BLAST.

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

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.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. 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. RNA and DNA are the proteins that store the 14 .

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

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

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

elegans genome project (funded by theMRC and NIH). as well as the C.000 current and withdrawn symbols).297 residues. GENEXPRESS (cDNA): catalogue the transcripts required for protein synthesis obtained from specific tissues. elegans data. This initial release contains the following kinds of information: Loci (over15. 18 . for example neuromuscular tissues. PCR primers (currently 500primer pairs). the C.000). can be obtained via ftp. Bibliography (over 18. ACeDB (A Caenorhabditis elegans Database): Containing data from the Caenorhabditis Genetics Center (funded by the NIH National Center for Research Resources). GENETIC MAP: production of micro-satellite probes and the localization of chromosomes.Bioinformatics 18 19. MGD: The Mouse Genome Databases: MGD is a comprehensive database of genetic information on the laboratory mouse. 3500 loci from 40 mammalian species). elegans. The software. PIR and Swiss Prot are primary databases that contain protein sequences as 'raw' data. ACeDB is also the name of the generic genome database software in use by an increasing number of genome projects. Drosophila melanogaster.000 references).747. Probes and Clones (about 10. Protein sequence databases are classified as primary. mycobacteria. and the worm community. Secondary databases (like Prosite) contain the information derived from protein sequences. secondary and composite depending upon the content stored in them. Experimental data (from 2400 published articles). ACeDB databases are available for the following species: C. HumanChromosome 21. Human Chromosome X. to create a genetic map to aid in the study of hereditary diseases. 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. Homologies (1300 mouse loci.

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

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

or the presence of only very conservative substitutions (that is. If two sequences in an alignment share a common an cestor. In protein sequence alignment. The absence of substitutions.Bioinformatics 21 A sequence alignment. such as those present in natural language or in financial data. 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. 21 . insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. the substitution of amino acids whose side chains have similar biochemical properties) in a particular region of the sequence. Sequence alignment canbe used for non-biological sequences. suggest that this region has structural or functional importance. Although DNA and RNA nucleotide bases are more similar to each other than to amino acids. produced by ClustalW between two human zinc finger proteins identified by GenBank accession number. mismatches can be interpreted as point mutations and gaps as indels (that is.

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

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

BioInformatics Tools The Bioinformatics tools are the software programs for the saving. Multiple alignments are often used in identifying conserved sequence regions across a group of sequences hypothesized to be evolutionarily related. Multiple alignment methods try to align all of the sequences in a given query set.Bioinformatics Multiple sequence alignment is an extension of pair wise alignment to incorporate more than two sequences at a time. These software tools must be made available over the internet given the global distribution of the scientific research community. retrieving and analysis of Biological data and extracting the information from them. 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. Multiple sequence alignments are computationally difficult to produce and most formulations of the problem lead to NP-complete combinatorial optimization problems. the utility of these alignments in bioinformatics has led to the development of a variety of methods suitable for aligning three or more sequences. • The Bioinformatics Tools may be categorized into following categories: • • • Homology and Similarity Tools Protein Function Analysis Structural Analysis 24 . 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. Nevertheless.

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

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

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

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

how many kinases in Yeast 29 .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.

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

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