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• Bioinformatics


  The use of computer to store, retrieve, analyse or predict the composition or structure of bio-molecules
• Bioinformatics is the application of computational techniques and information technology to the organisation and management of biological data
• Classical bioinformatics deals primarily with sequence analysis
• Aims of bioinformatics


  • Development of database containing all biological information
  • Development of better tools for data designing, annotation and mining
  • Design and development of drugs by using simulation software
  • Design and development of software tools for protein structure prediction function, annotation and docking analysis
  • Creation and development of software to improve tools for analysing sequences for their function and similarity with other sequences
• Applications of bioinformatics


  • Gene therapy
  • Drug designing
  • Antibiotic resistance
  • Crop development
  • Medicine biotechnology
  • Drought resistance
  • Evolutionary studies
  • Forensic analysis
  • Veterinary science
  • Weather analysis
  • Waste cleanup
• Biological database


  A collection of biological data arranged in computer readable form that enhances the speed of search and retrieval and convenient to use
• Biological data are complex, exception-ridden, vast and incomplete
• A good database must have updated information
• Importance of biological database


  • Retrieve a range of information like biological sequences, structures, binding sites, metabolic interactions, molecular action, functional relationships, protein families, motifs and homologous
• Types of biological database

  • Nucleotide sequence database
  • Protein sequence database
  • Structure database
  • Domain and motif database
  • Gene expression database
  • Metabolic pathway database
• Primary database


  Contains only sequence or structural information
• Secondary database


  Derived from the analysis or treatment of primary data
• Secondary databases are very important for inferring protein function
• GeneBank


  One of the fastest growing repositories of known nucleotide sequences, has a flat file structure, readable by both humans and computers
• GeneBank contains information such as accession numbers and gene names, phylogenetic classification and references to published literature
• GeneBank has been developed and maintained at the NCBI, Bethesda, MD, USA, as a part of International Sequence Database Collaboration (INSDC)
• GeneBank is an open access sequence database
• GeneBank coordinates with individual laboratories and other sequence databases like EMBL and DDBJ
• GeneBank is an annotated collection of all nucleotide sequences that are available to the public
• The nucleotide database was divided into three databases at NCBI: CoreNucleotide database, Expressed Sequence Tag (EST) and Genome Survey Sequence (GSS)
• CoreNucleotide database has most of the nucleotide sequences used. It also encloses all nucleotide records that are not in the EST and GSS databases
• Submission of sequences to GeneBank can be done using BankIt, Sequin and tbl2asn tools
• EMBL (European Molecular Biology Laboratory)


  A comprehensive database of DNA and RNA sequences, collected from scientific literature, patient offices and is directly submitted by researchers
• EMBL has been prepared in collaboration with GeneBank (USA) and the DNA Database of Japan (DDBJ)
• EMBL is established in 1980 and maintained by EBI (European Bioinformatics Institute)
• Swiss-Port


  A curated protein sequence database that offers a high level of integration with other databases and also has a very low level of redundancy
• Swiss-Port strives to provide protein sequences with a high level of annotation (for instance, the description of protein function, domain structure and post translational modifications, etc.)
• Swiss-Port is established in 1986 and maintained collaboratively, since 1987, by the department of Medical Biochemistry of the University of Geneva and the EMBL data Library
• TrEMBL is a computer–annotated supplement of Swiss-Port that contains all translations of EMBL nucleotide sequence entries, which is not yet integrated in Swiss-Port
• Currently Swiss-Port have 0.5 and TrEMBL have 7.6 million sequences
• Protein Information Resource (PIR)

  An integrated public bioinformatics resource to support genomic and proteomic research and scientific studies
• PIR offers a wide variety of resources mainly oriented to assisting the propagation and consistency of protein annotations like PIRSF, ProClass and ProLINK
• Protein sequence motif


  A set of conserved amino acid residues that are important for protein function and are located within a certain distance from one another
• PROSITE database


  Consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them
• PRINT


  A database for protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family
• Protein domain


  An independently folded, structurally compact unit that forms a steady three-dimensional structure and shows a certain level of evolutionary conservation
• ProDom


  A protein domain database automatically generated from the Swiss-Port and TrEMBL sequence database
• SMART


  A highly reliable and sensitive tool for domain identification
• COG


  A database and a convenient tool for motif and domain identification
• PDB (Protein Data Bank)

  The main primary database for 3D structures of biological macromolecules determined by X-ray, crystallography and NMR