2 BIOLOGICAL DATA AND DATABASE, Biological Data ‘The data that are collected from biological world are called biological data. For example, DNA sequence data, population data, genetical data, ecological data ete. However, bioinformatics deals with biomolecule’s related data collected from scientific experiments, published literatures and computational analyses. With the advent of new techniques and computational tools there is an exponential increase of information on biomolecules. Bioinformaticists store these biological data (data on DNA, RNA and protein) in digitalize form i.e. in database, For world wide data submission and management, access, exchange through intemet bioinformaticists constructed databases where data on biomolecules are stored in systematically. Till date vast range of databases have been constructed by the bioinformaticists and made accessible through internet for the researchers. The databases include DNA, RNA and protein sequence data, structural information, gene expression data, molecular interaction data, mutation data, phenotypic data, metabolic pathways information, taxonomic information of biological organism etc. Biological Database The Biological data can be broadly classified as: Biological Databases Information they contain 1. Bibliographic databases Literature 2. Taxonomic databases Classification 3. Nucleic acid databases DNA information 4, Genomic databases Gene level information 5. Protein databases Protein information 6. Protein families, domains and functional sites Classification of proteins and identifying domains 7. Enzymes/ metabolic pathways Metabolic pathways Biological databases act as repository of biological information for utilization by researchers. The biological database is a collection of "entry" which is the unit of the data, Each entry includes nucleotide sequence data, protein sequence and 3D structure data, the biological nature such as gene function and other property of the sequence ete. and the information of submitters, references, source organisms. Biological databases are coherent, consistent and designed for a specific purpose to store a set of clearly defined data in an organized manner. The contents of database can easily be accessed, managed and updated, The contents of database can be analyzed with the help of defined algorithm. The biological databases are of various types which can be outlined as follows —Biological Database v v alae seeyty compose owns Sequence ee ee Gehome inure Paty database database related related related information information information _—information DNA/nucleotide Protein | (a database database Organism Literature based Biodiversity Specific database information informatics database (Non-human) Fig, 2.1: Classification of biological databases. A, Primary Database Primary databases are repository of raw sequenced and annotated data that derived experimentally such as nucleotide sequences, three dimensional structures of protein and signifies important properties of each sequence. These primary databases can be accessed freely through internet over World Wide Web (W.W.W). Primary databases can be further classified as given below, ~ 1. Sequence database: Sequence database stores information on sequence of DNA/nucleotide and protein. i. DNA/nucleotide database: DNA/nucleotide databases stores data on DNA/nucleotide sequence. Each database maintains an own set of submission and retrieval tools, but they exchange data daily so that all the databases should contain the same set of sequences. Some important examples of DNA/nucleotide databases are given below, — GenBank Et GenBank sequence database is an open access and annotated collection < y of nucleotide sequences and their ~=—protein —_translations Seung mRNA sores with coding regions, segments of } genomic DNA with a single gene or multiple genes, and ribosomal RNA gene NCBI ciusters. GenBank is produced and maintained by the National Centre for Biotechnology Information (NCBI) as part of the International collaboration with EMBL Data Library from the EBI and the DNA Data Bank of Japan (DDBJ). Individual laboratory can submit sequence data or large scale sequencing centre can submit bulk submission directly to the GenBank by using Banklt or Sequin. The Banklt is a web- based form and Sequin is a stand-alone software tool developed by the NCBI for submitting and updating sequence to the GenBank, EMBL and DDBJ databases. After sequence submission the GenBank staffs assigns an Accession Number to the newly entered sequenceand performs quality assurance checks. Then the newly submitted sequence is released to the Gatabase, Data that are stored in GenBank can be retrieved by Entrez or by downloading File Transfer Protocol (FTP), The GenBank is a collection of information on Expressed Sequence Tag (EST), Sequence Tagged Site (STS), Genome Survey Sequence (GSS), and High- Throughput Genome Sequence (HTGS) and complete microbial genome sequences. Information of GenBank canbe accessed ~— through the — server |hutp-/Avww.nebi.nlm.nih.gov/genbanl/. There are several ways to search and retrieve data from GenBank as given under — * Search GenBank for sequence identifiers and annotations with Entrez Nucleotide , which is divided into. three divisions: CoreNucleotide (the main collection), dbEST (Expressed Sequence Tags), and dbGSS (Genome Survey Sequences), * Search and align GenBank sequences to a query sequence using BLAST. * Search, link, and download sequences programmatically using NCBI e-utilities . DNA Data Bank of Japan (DDBJ) & DDB is a kind of nucleotide sequence data bank that receives Ye LS Psi, nucleotide sequence from researchers and assigns an accession PEE umber to data submitters, DDBY collects sequence data mainly from Japanese researchers, however, they also receive data and assign accession number to researchers of any other countries. DDBJ began data bank activities in 1986 at National Institute of Genetics (NIG). Currently, DDBJ is in operation at NIG in Mishima, Tapan. Main activities of DDBJ are ~ i) being a member of INSDC, DDBJ collects nucleotide sequence data from researcher, assigns an accession number to the data submitters exchanges the collected data with EMBL-Bank and GenBank on a daily basis, ii) DDBJ manage bioinformatics tools for data submission and retrieval, iii) DDBJ develops tools for analysis of biological data and —_iv) organizes Bioinformatics Training Course in Japanese to teach how to analyze biological data. Information of DDBJ can be accessed through the server http://www.ddb; European Molecular Biology Laboratory- European Bioinformatics Institute (EMBL- EBD) European Bioinformatics Institute (EBI) is part of European Molecular Biology Laboratory (EMBL). EMBL-EBI now known as EMBL-Bank and was established in 1980 at the EMBL in Heidelberg, Germany. It was the world’s first nucleotide sequence database. EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme for the researchers, EMBL-EBI Stores data on DNA and RNA (genes, genomes and variation), gene expression (RNA, Protein and metabolite expression), protein (sequence, families and motifs), structure (molecular and cellular structures), systems (feaction, interaction, pathways), chemical biology (chemogenomics and metabolomics), ontologies (taxonomies and controlled ‘ocabularies) and literature (scientific publications and patents), EMBL-EBI can be accessed through the server. bttp://www.ebi.ac.uk,EnsEMBL Ensembl is a joint project between EBI, EMBL and the that itute to develop a software system PAE Ta| Welcome Trust Sanger Institute t0 b eel produces ‘and maintains automatically annotation on selected it ‘cally annotate the eukaryotic genomes, EnsEMBL was stated in 1999 with an aim to eeoicel a - genome, integrate this annotation with other available biological oe information to the researchers via the web. EnsEMBL produces genome daisbasst, vertebrates and other eukaryotic species and makes this information freely availat a EnsEMBL can be freely accessed through the server http:/www.asia.ensembl.org. arous research projects around the world contribute DNA sequence and their assemblies data to EnsEMBL. This database emphasizes on two areas of comparative genomics — the creation of gene trees using representative proteins from each gene in a species, and the alignment of DNA sequences to infer synteny, conservation, etc. The Ensembl Variation database stores data on the regions of genome that differ between individual genomes, associated disease and Phenotype information. Ensembl Regulation stores data on the mechanisms of gene regulation in human and mouse célls, transcriptional and post-transcriptional mechanisms. ii, Protein database: Primary protein sequence databases store information on protein sequence. Some primary protein sequence databases are briefly describe hereunder — Protein Information Resource (PIR) PIR was developed by the National Biomedical Research Foundation (NBRF) in fap] 1984 to assist researchers in the identification and interpretation of protein sequence information, It is an integrated public resource of protein informatics that supports genomic and proteomic research and scientific discovery. PIR has three distinct sections ~ PIRI contains fully classified and annotated entries, PIR2 contains preliminary entries that has not been thoroughly reviewed and contain redundancy, PIR3 contain unverified entries and PIR4 has one of the following categories ~ i. conceptual translations of art factual sequences, ii, conceptual translations of sequences that are not transcribed or translated, ii. protein sequences or conceptual translations that are genetically engineered, iv. Sequences that are not genetically encoded and not produced on ribosomes. PIR maintains the Protein Sequence Database (PSD) that stores over 283 000 sequences, For over four decades PIR has been providing protein databases and analysis tools those are freely accessible to the researchers including the Protein Sequence Database (PSD). The PIR has a bibliography system for literature searching, mapping, and user submission. PIR also maintains (Non- redundant Reference) NREF database, and iProClass, an integrated database of protein family, function and structure information, PIR-NREF protein sequences information, Currently it is consisting of more than 1 000 000 entries from PIR-PSD, SWISS-PROT. TEMBL, RefSeq, GenPept, and PDB. ‘The PIR web site ig hup:/www pir georgetown.edu,UniProtKB/Swiss-Prot subd UniProtKB/SwissProt is the manually annotated and reviewed section of the UniProt knowledgebase (UniProtKB), It is an annotated and non-redundant (means less ‘identical sequences are present in the database) protein sequence database, Swiss-Prot was established in 1986 and maintained collaboratively by the EMBL Outstation (EBI) and the ‘Swiss Institute of Bioinformatics (SIB). It provides information on domain structure of protein, its function, post-translational modification, variants etc. The Swiss-Prot database distinguishes itself from other protein sequence databases by three distinct criteria ~ i. annotation, ii. minimal redundancy and ii, integration with other databases. In 1996, a computerannotated supplement to SWISS-PORT was created and named as TeEMBL (Translation of EMBL nucleotide sequence database). TrEMBL consists of computer annotated entries derived from the translation of all coding sequence (CDSs) in the EMBL database except for CDSs already present in Swiss-Prot (Bairoch and Apweiler, 2000). The server for SwissProt and TrEMBL are www.ebi.ac.uk/uniprot and www.ebi.ac.uk respectively. Protein Sequence Database (PSD) PIR-Intemnational Protein Sequence Database (PIR-PSD), the world's first database of classified and functionally annotated protein sequences that grew out of the Atlas of Protein Sequence and Structure (1965-1978) edited by Margaret Dayhoff. It is produced and distributed by the Protein Information Resource in collaboration with MIPS (Munich Information Center for Protein Sequences) and JIPID (Japan International Protein Information Database). PIR-PSD has been the most comprehensive and expertly-curated protein sequence database for over 20 years. The URL for PSD is http:// www pir georgetown.edu, 2. Structure database: Structure databases are created to store structure information of biological macromolecules e.g. nucleic acid and protein. Some important structure databases are given here under — Protein Data Bank (PDB) 3 Protein Data Bank was established at Brookhaven National FEorriw nave nave Laboratories (BNL) in 1971. PDB contains 3D structure of protein that is established by x-ray crystallographic and nuclear magnetic resonance (NMR) studies and is maintained by Research Collaboratory for Structural Bioinformatics (RCSB) at Rutgers University. As on December 24, 2013 there are 96596 structures of proteins available at PDB whose provide information on atomic co-ordinate of amino acids in protein, protein fragments or protein bound to substrate or inhibitors, Protein structure data can be deposited in the PDB using a web-based AutoDep Input Tool (ADIT). Molecular structure of protein of PDB can be displayed by molecular graphics program such as Resnol, Chine CnED (Bansal, 2009). PDB’s URL is hitp://www.resb.org/pdb/.ic Acid Database (NDB) ‘Nucleic Acid Database is a comprehensive database of 3D ids. The goal of the Nucleic Acid Database Project en structures of nucleic aci C Pr mlm (NDB) isto store and distribute structural information about nucleic acids, M. Berman and Wilma K. Olson of Rutgers Nuclei ‘The NDB was founded in 1992 by Helen ” University and David Beveridge of Wesleyan University. Cambridge Crystallographic Data Centre/Cambridge Structural Database (CCDB/CSD) ; Cambridge Crystallographic Data Centre (CCDC) is a QOOE costatographic non-profit organisation that is situated in Cambridge, vmuicesecamaeax England. It compiles and distributes the Cambridge Structural Database (CSD). CSD is a database of small molecules. organic and metal-organic crystal structural data. CSD’s URL is www.cede.cam.ac.uk. It stores experimentally determined B. Secondary database “The secondary database contains the data of analyses of the primary sequence data in form of regular pattern, fingerprints, blocks, profiles or Hidden Markov Model. Thus, the secondary database contains the fruit of analyses of the sequences stored in the primary database and contains information about conserved sequence, signature sequence, active site residues of protein families arrived by multiple sequence alignment of a set of related proteins. ProSite, Profiles, Prints, Pfam, REBase etc, are some examples of secondary database. Secondary database falls under four categories sequence related database, genome related database, structure related database and pathway database. 1, Sequence related database ProSite ores g ProSite is a secondary protein database and contains information of protein families, domains, functional sites as well as amino acid pattern and profile of protein. These information are manually curated by a team of the Swiss Institute of Bioinformatics. ProSite was created by Amos Bairoch in 1988. ProSite offers tools for protein sequence analysis and motif detection, The database ProRule builds on the domain description of ProSite (Sigrist et al, 2005). It provides information about structurally and functionally critical amino acid. The URL for ProSite is htp://www.prosite expasy.org. Pfam Pfam Pfam is a database of protein families that provides multiple sequence alignment and Hidden Markov Models (HMM) for protein domains of all types of organisms. Information on multiple sequence alignment is generated by using HMM (Finn et al, 2008: Finn et al, 2006 and Bateman er al, 2005). Pfam can be searched for multiple sequenceyy” alignment, protein domain structure, to examine species distribution, to follow other databases and to view known protein structure, The Pfam has two components. Pfam-A_ stores manually curated high quality entries, For each entry a protein sequence alignment and. a HMM is stored, Automatically generated lower quality entries are stored in Pfam-B- Entries in Pfam-A do not cover all known proteins, in that case lower quality Pfam-B families can be used. ExplorEnz ExplorBnz is an open access, manually curated and peer reviewed enzyme database. Exploriinz is designed, developed and maintained by Andrew MeDonald at School of Biochemistry and Immunology, Trinity College, Dublin, Ireland to access the data of the International Union of Biochemistry and Molecular Biology (TUBMB) enzyme nomenclature list. REBase REBasr? REBase is the restriction enzyme database. It is maintained by Richard I. Roberts since before 1980 (Roberts, 1980). It stores information about restriction enzymes and related proteins, published and unpublished references, recognition and cleavage sites isoschizomers, commercial availability, methylation sensitivity, crystal, genome, sequence data, DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins. The official website for REBase is http://www.rebase.neb.com, 2. Genome related database ‘Online Mendelian Inheritance in Man (OMIM) OMIM is a database that stores informations of human genes and genetic disorders, genetic variation in human and pictures. It also provides references for further research and tools for genomic analysis of a catalogued gene (Hamosh, 2004). Mendelian Inheritance in ‘Man (MIM) was started in the early 1960s and is available in form of book. The online version i.e. OMIM has been available since 1987 (McKusick, 1993). The information in OMIM is collected and processed under the leadership of Dr. Victor A. McKiusick at Johns Hopkins University, assisted by a team of science writers and editors. A six digit number is assigned against every disease and gene of which the first number classifies the method of inheritance. The initial digit 1 signifies autosomal dominant trait; 2, signifies autosomal recessive trait; 3, signifies X-linked trait; a number symbol (#) before an entry number indicates that itis a descriptive entry; a plus sign (+) before an entry number indicates that the entry contains the description of a gene of known sequence and a phenotype; a percent sign (%o) before an entry number indicates that the entry describes a confirmed Mendelian phenotype or phenotypic locus for which the underlying molecular basis is not known; no symbol before an entry number indicates a description of a phenotype for which the Mendelian basis has not been clearly established and a caret (‘) before an entry number means the entry no longer exists because it was removed from the database or moved to another entry (http:/www.omim.org/help/fagi.2).Plant Transcription Factor Database (PinTFDB) 11 plant genes involved in is a public database that identifies and stores all kadar st Jant ‘Transcription ‘Factor ‘Database tanscipional control, The Plant Transrpton || Fain || ‘DB; http://plntfab.bio.uni-potsdam.de/v3.0/) is an integra 1 rican tional regulators (TRs) in plant complete sets of transcription factors (TFs) and other transcrip! pei) species whose genomes have ben completely sequenced and annotated, "he compte Hes o& 84 fales of TFs and TRs fom 19 species ranging fom unicellular red and green algae 19 angiosperms are included in PlnTFDB, representing >16 billion years of evolution of gen regulatory networks. TF or TR gene enties include information of expressed sequence 8s, 3D protein sutures of homologous proteins, domain architecture and erossinks 0 over computational resources online. Moreover, the different species in PlnTFDB are linked to each other by means of orthologous genes facilitating cross-species comparisons. (Paulino, 2010). 3. Structure related database Database of Secondary Structure Assignments (DSSP) The DSSP program was designed by Wolfgang Kabsch and Chris Sander for standardization of secondary structure assignment. Basically DSSP is a database of secondary structure assignments for all protein entries in the Protein Data Bank (PDB). DSSP does not predict secondary structure. Homology-derived Secondary Structure of Proteins (HSSP) HSSP was designed by Chris Sander and Reinhard Schneider. For each know protein structure the database contains the aligned sequence, secondary structure, sequence variability and sequence profile (Sander and Schneider, 1991), HSSP also implies tertiary structure of protein. Families of Structurally Similar Proteins (FSSP) FSSP is a database of structurally similiar proteins generated using the "Distance- matrix Alignment” (DALI) algorithm. The database is helpful for the comparison of protein structures. Dali database Dali is the secondary structure database, based on comparison of 3D protein structures of Protein Data Bank (PDB). 4. Pathway information database Pathway information database provide information on molecular interaction in biological process, information about genes and proteins and information about the chemical compounds and their reactions,C. Composite database Composite databases store data of different primary databases, thus 0 jaa i ice, protein to search multiple primary databases for nucleotide sequence, protein sequence, P structure ete, Examples of some composite databases are — 1, nrdb (nonredundant database) combines and stores sequences fro translations), PDB, Swiss-Prot, PIR, and PRE. i of PIR, ences 2. INSD (International Nucleotide Sequence Database) stores nucleotide seq EMBL, GenBank, and DDBI. . : es from 3. UniProt (universal protein sequence database) is a collection of protein sequen! PIR-PSD, Swiss-Prot, and TEMBL. ym GenBank (CDS D, Others Other databases includes organism specific database, literature based database and biodiversity informatics database. Organism specific databases provide information on various organisms other than human like- virus, bacteria, fungi, invertebrates, Drosophilé, beetle, silkworm ete. Organism specific databases store information on genome of respective organism, genome map, gene expression, genomic mutation of Drosophila, morphologica features of Yeast, growth requirements of bacterial pathogen etc. Literature based database contain scientific articles in form of abstract or full paper published by researchers in Gifferent journals, There are several high quality literature based databases but the most popular is PubMed. Biodiversity informatics databases contain information on biodiversity of different organisms. Biological database retrieval system ‘There are three important data retrieval systems: Entrez (at NCBI), Sequence Retrieval System, SRS (at EBD) and DBGET/LinkDB (at Japan). These retrieval systems not only return matches to a query, but also provide additional important information in related databases. ENTREZ, Entrez is a molecular biology database and retrieval system developed by the National Center for Biotechnology Information (NCBI). It can be accessed through hup://www.ncbi.nlm.nih.gov/Entrez/, The Entrez system provides access to Nucleotide sequence databases — GenBank/DDBW/EBI; Protein sequence databases - Swiss-Prot, PIR, PRE, PDB, and translated protein sequences from DNA sequence databases; Genome and chromosome mapping data; Molecular Modeling 3-D structures Database; Literature database, PubMed - provides access to MEDLINE and pte-MEDLINE articles; Taxonomy database - allows retrieval of DNA and protein sequences for different taxonomic groups; Specialized Databases — OMIM, dbSNP, UniSTS, etc. ‘The most valuable feature of Entrez is- by exploiting the concept of ‘neighbouring? it Provides access to related articles of linked databases. For example, in a nucleotide sequence age, one may find cross-referencing links to the translated protein sequence, : genome mapping data or to the related PubMed literature information and to protein structures if10 2006), Another useful feature in Entrez, is ~ one can retrieve large sets of available (Xiong, pi data on the basis of some criterion and can download them to a local comp\ ‘Sequence Retrieval System (SRS) ; ; aarerThe SRS isa network browser for databases in molecular biology. Tt can be accessed through http://srs.ebi.ac.uk/. SRS searches 80 biological databases developed at the European Bioinformatics Institute (EBD at Hinxton, UK. It provides access to sequence and sequence related, metabolic pathways, transcription factors, application results (¢.g., BLAST), protein 3D-structure, genome, mapping, mutations, and locus-specific mutations databases. Advantage of SRS is that it rapidly searches query, allowing users to retrieve, link and ‘access entries from all the interconnected resources. DBGET/LinkDB It is an integrated bioinformatics database retrieval system at GenomeNet, developed by the Institute for Chemical Research, Kyoto University, and the Human Genome Center of re university of Tokyo. It can be accessed through hitpi//uww.senome.ad.jp/dbget/, DBGET provides access to about 20 molecular biology databases, which can be queried one at time, After querying one of database, DBGET provides links to associate information in Addition to the lst of results. A unique feature of DBGET is its connection with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database - a database of metabolic and regulatory pathways nexBranches of Bioinformatics: The scier ii s ience of bioinformatics ean be divided into several branches based on the experimental a . ‘ : ma terial used for the study, Bioinformatics is broadly divided into two groups, Vi2~ animal ioinformatics and plant bioinformatics, Various branches of bioinformatics are defined below: 1. Animal Bioinformatics: It deals with computer added study of genomics, proteomics and rmetabolomics in various animal species, Tt includes study of gene mapping, gene sequencing, animal breeds, animal genetic resources etc. It can be further divided as joinformatics of mammals reptiles, insects, birds, fishes etc. 2. Plant Bioinformatics: It deals with computer aided study of plant species. It includes gene mapping, gene sequencing, plant genetic resources, data base ete. It-can be further divided into following branches: @) Agricultural Bioinformatics: It deals with computer based study of various agricultural crop species. It is also referred to as crop bioinformatics. (i) Mortcultural Bioinformatics: It refers to computer aided study of horticultural crops, viz. fruit crops, vegetable crops and flower crops. (ii) Medicinal Plants Bioinformatics: It deals with computer based study of various medicinal plant species. "Gv Forest Plant Bioinformatics: I deals with computer based study of forest plant species [A living cell is a system with cellular components interacting with each other, and these Jnteractions determine the fate of the cell, e.g., whether a stem cell is going to become a liver tell, or a cancer cel. These interacting components include- the genome, the gene transcript and the proteins. Characterization of these three types of components and the associated development of analytical methods lead to the establishment of the three closely related branches of bioinformatics-Genomics, Transcriptomies and Proteomics. Genomics involves extensive analysis of nucleic acids through molecular biological techniques, before the data are ready for processing by computers. Genomics is a science that attempts to describe a living organism in terms of the sequence of its genome (its constituent genetic material). Proteomics represent the earliest attempt to identify a major subclass of cellular components, the proteins and their interactions, It has been coined from the word “proteome” which is the complete protein complement of a system. Proteomics involves the sequencing of amino acids in a protein, determining its three-dimensional structure and relating it to the function of the protein. Before computer processing comes into the picture, extensive data, particularly through crystallography and NMR, are required for this kind of a study. With such data on known proteins, the structure and its relationship to function of newly discovered proteins can be understood in a very short time. In such areas, bioinformatics has an enormous analytical7 ntifying when and where proteins are in an organism. i jomics also focuses on i 1d predictive potential. Proteomics al s capresed in a cell so as to establish their physiological roles i expression level of genes, often using techniques capable of different mRNA molecules at a time (eg DNA microarrays). he word - Transcriptome which is the set of all Jation of biological cells for a given set of ‘Transeriptomies depicts the sampling tens of thousands of ‘Transeriptomies has been coined from th mRNA molecules (or transcripts) in one or a popu environmental circumstances. ‘Apart from these there are few major branches mentioned below: Functional Genomics: Since the completion of the human genome, the emphasis has been changing from genes themselves to gene products. Functional genomics assigns functional relevance to genomic information. It is the study of genes, their resulting proteins, and the role played by the proteins. Cheminformaties: Drug design through bioinformatics is one of the most actively pursued areas of research. Since a great majority of drugs are LMW (Low Molecular Weight) compounds and since many of them are primarily derived from biological sources, there has always been a great interest in the study of LMW compounds of biological origin. Cheminformatics (or chemoinformatics) deals with such compounds, the products of secondary metabolism, often called natural products which has some kind of bioreactivity. This bioactivity can be turned to advantage for therapeutic purposes. Here the expertise of a pharmacologist is required. Cheminformatics involves organisation of chemical data in @ logical form to facilitate the process of understanding chemical properties, their relationship to structures and making inferences. Chemical structures are the input to identify similar compounds for screening for biological activity. It also helps to assess the properties of new ‘compounds, by comparison with the known compounds. Aim of Bioinformatics Aim of bioinformatics are given here under ~ 1. Storage of biological data in form of databases to facilitate easy retrieval and ~ submission of new entries of biological information by researchers. 2. Development of tools and resources for data analysis. For example BLASTto find out similar nucleotide/amino acid sequences, ClustalW to. align two or more nucleotide/amino acid sequences and Primer3 to design primer probes for PCR techniques etc. 3. Exploitation of computational tools to analyse the biological data and interpret the analysed data in a biologically meaningful manner, Scope of Bioinformaticsa Biote sowan tealoy i ew ad excking bach of tech. ily ea i setened i Nas range of Wolgia dats toed in databases that ae experimentally foment ioinformatics processes data on gene sequencing that is Frings blotechnal hnologists and makes the information accessible forthe researchers, This ieee leay thin the dimension of bioinformatics, Bioinformatics involves Tetieve, lac aed and computer science, In bioinformatics computer is required to store, Tehelelad \yse/predict the composition or structure of the biomolecules. Presently in formaties emphasis has been given on genome research, human genome sequencing, Grug design and other disease related issues. It covers important sectors of human life viz. agriculture, health, environment etc. ___ Scope means area of study. Its obvious that bioinformatics has a very wide scope as given under — Computational Bioinformatics It involves computational works to develop an application for deating biological problems. ‘Computational bioinformatics deals with development of algorithm and software. Algorithm is a logical sequence of steps by which a task can be performed. Molecular biologists, bioinformaticist, computer scientist, system engineer, mathematicians or statistician work together to solve biological problem by designing an algorithm. Another important aspect of computational bioinformatics is database construction and curation. Vast range of information thet have generated by biotechnological works on genome, protein and other biomolecules of various organisms are stored in respective databases. The data that are stored in databases are annotated and can be easily retrieved by researchers. There are countless public databases that store different level of biological information. Application Bioinformatics “Another exciting study area of bioinformatics is application bioinformatics Application bioinformatics deals with sequence analysis, structureanalysis and function ‘analysis of biomolecules. With the help of computer'_—_—program biolnformaticisVbioinformatician analyses the sequence of biomolecules like DNA, RNA and protein, Analysis of the sequence of biomolecules is done for evolutionary analysis, dentification of mutations, identification of exon and introns, identification and ‘Characterization of novel microbes, selection of drug and its appropriate dose for a patient, identification of drug target and gene therapy ete. Structure analysis deals with analysis of structure of unknown protein or nucleic acid by comparing the structure of these unknown biomolecules with the known structures stored in structure databases. It facilitates determination of 2D or 3D structure of proteins and nucleic acids and thus helps in prediction of their function, Function analysis deals with determination of function of gene or protein ‘with the help of function databases. It promotes use of annotated gene or protein for human welfare by biotechnological means. What is bioinformatics? A proposed definition and overview of the field. NM Luscombe, D Greenbaum, M Gerstein (2001) Methods Inf Med 40: 346-58 .