Database in bioinformatics

database in bioinformatics

1. Database A Computerized archive used to store and organize data in such a way that information can be retrieved easily. A database is a repository of information that has a specific structure that enables the entering and extraction of data In general this database structure consists of files or tables, each containing numerous records and fields

2. Conti.. Database System (DBS) is an integrated collection of related files along with the detail about their definition, interpretation, manipulation and maintenance A database system is based on the data. Also a database system can be run or executed by using software called DBMS (Database Management System). A database system controls the data from unauthorized access. A database management system (DBMS) is a collection of programs that enables users to create and maintain a database.

3. Database management systems Database management systems provide several functions in addition to simple file management: control security maintain data integrity provide for backup and recovery control redundancy allow data independence provide non-procedural query language perform automatic query optimization

4. Organisation Organisation: flat files Relational databases Flat-file databases the simplest form of a database, where collections of data, such as nucleotide and amino acid sequence, are stored as either a large single text file

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6. Conti.. a database that treats all of its data as a collection of relations A relational database stores the data within a number of tables. Each table consists of records and fields (rows and columns)

7. Types of Database The databases can be classified into three categories on the basis of the information stored. They are Primary, Secondary and Composite databases. Primary databases contain data that is derived experimentally. They usually store information related to the sequences or structures of biological components They can be further divided into protein or nucleotide databases

8. Primary Database This databases contains the raw nucleic acid sequence data which are produced and submitted by researchers worldwide. NCBI(The National Centre for Biotechnology Information) GenBank DDBJ (DNA data bank of Japan) SWISS-PROT(Swiss- Prot ) PIR (Protein Information Resource) PDB(Protein Data Bank) TrEMBL (Translated European Molecular Biology Laboratory) Protein PIR MIPS SWISS-PROT TrEMBL

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10. Secondary Databases Secondary Databases: contain information derived from primary databases. store information such as conserved sequences, active site residues, and signature sequences. Protein Databank data is stored in secondary databases. Examples include: Class Architecture Topology Homology (CATH), Kyoto Encyclopedia of Genes and Genomics (KEGG), Protein Families ( Pfam ) and Structural Classification of Proteins (SCOP)

11. Composite Databases Composite Databases are collections of several primary database resources. provide users with various tools and software for analysis of data. NCBI being a composite database has stored a lot of sequence of nucleotide and protein within its server and thereby suffers from high redundancy in the data deposited

12. Biological databases Biological databases can be broadly classified in to Sequence database structure database and pathway databases. Sequence databases are applicable to both nucleic acid sequences and protein sequences, whereas structure databases are applicable to only Proteins.

13. Sequence databases Sequence databases Nucleotide and protein sequence databases represent the most widely used and some of the best established biological databases. serve as repositories for wet lab results and the primary source for experimental results. Major public data banks included in this type are GenBank in USA, EMBL (European Molecular Biology Laboratory) in Europe and DDBJ ( DNADataBank ) in Japan

14. Conti…. And protein databases includes ExPaSy UniProt PIR PDB Swiss- Prot TrEMBL

15. NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION (NCBI) developed at the National Institutes of Health (NIH) in 1988 Part of national library of medicine at national institute of health provides access to a large amount of biomedical and genomic information ( www.ncbi.nlm.nih.gov/home/ about/mission.shtml). It maintains a large scale of databases and bioinformatics tools as well as services. One of the most popular databases is GenBank

16. Conti… Mission or role The aim is to find novel techniques and methodologies for dealing with huge and complex data and provide better accessibility to analytical and computational tools. Maintenance of biological databases whether primary or secondary. It includes GENEBANK NCBI provides the data retrieval systems such as ENTREZ Provides computational sources for the analysis of the GENEBANK data and other biological data

17. Conti… Resources The resources that are present on this site can be divided into two major categories: 1) databases 2) tools

18. The major databases maintained at NCBI are GenBank and PubMed (bibliographic database for biomedical literature). Other databases include the Gene, Genome, Epigenomics, Gene Expression RefSeq , Structure, Database of Short Genetic Variation ( dbSNP ), TAXONOMY, etc.

19. TOOLS at NCBI The NCBI also provides a variety of tools for database search The Entrez: is search engine of NCBI The other tools include Genomes Browser, BLAST, CDTree , Genetic Codes, Open Reading Frame Finder (ORF Finder), SNP Database Specialized Search Tools,

20. GenBank GenBank (Genetic Sequence Databank) GenBank® is the genetic sequence database at the National Center for Biotechnology Information (NCBI). It was established in the year 1982 and now maintained by the National Center for Biotechnology (NCBI). It contains publicly available nucleotide sequences DNA sequences can be submitted to GenBank using several different methods. BankIt: Web-based form for submission of a small number of sequences Sequin : More appropriate for complicated submissions containing many sequences

21. Structure of Genbank A detailed structure of a nucleotide sequence file format in this database includes the following: 1. Locus: This can be defined as a title given by GenBank itself to name the sequence entry. It includes the following: a. Locus Name: Similar to accession number for the sequence. b. Sequence Length: Tells the number of bases existing in the sequence.

22. Conti…. c. Molecule-Type: Identifies the type of nucleic acid sequence. The various types are mRNA (which is present as cDNA), rRNA, snRNA, and DNA. d. GB Division: Postulates class of the data according to classification criteria of GenBank. e. Modification Date: The date on which the record was modified.

23. 2. Definition: This denotes the name of the nucleotide sequence. 3. Accession: This covers accession number, accession version, and GI number. Accession number can be defined as the unique identifier associated with each nucleotide sequence present in the database. 4. VERSION - Identification number assigned to a single, specific sequence in the database. This number is in the format “ accession.version .” 5. GI Also a sequence identification number. Whenever a sequence is changed, the version number is increased and a new GI is assigned.

24. 6. Keyword: Defined words that were used to index the entries. 7. The Source: This describes organism from which sequences have been obtained. 8. Organism - The scientific name (usually genus and species) and phylogenetic lineage 9. REFERENCE - Citations of publications by sequence authors, the journal from which with the sequence was derived

25. 10. Features: These consist of the information derived from the sequence such as biological source, exon, intron, promoters, CDS alternate splice, Base Count, Origin

26. European Molecular Biology Laboratory (EMBL) The EMBL Nucleotide Sequence Database is maintained by EBI, UK It was formed in the year 1974 It develops and maintains a large number of databases, and scientists can access the data free of cost. This database serves as the primary source of nucleotide sequences for Europe. in this database, the nucleotide sequence data generated by large-scale genome-sequencing projects and those available from the European Patent Office can be submitted

27. Conti… Data collection is done in collaboration with GenBank (USA) and the DNA Database of Japan (DDBJ). The other genomic databases held at EBI are Ensembl (a database of genome annotation) Genome Reviews. The daily releases of the database contain new submissions and updated sequence data while every 3 months the entire database is released.

28. DDBJ DDBJ: DNA Data Bank of Japan Is a biological database that collects DNA sequences submitted by researchers. It is run by the National Institute of Genetics, Japan. DDBJ Flat File Format The data submitted in DDBJ is managed and retrieved according to the DDBJ format (flat file). The flat file includes the sequence and the information of who submitted the data, references, source organisms, and information about the feature, etc

29. Ensembl Genome Database Ensembl is one of several well known genome browsers for the retrieval of genomic information from several organisms including human, plants, bacteria and animals. Created and maintained by the EBI and the Sanger Center (UK)

30. databases for green plants There are three different comparative genomic databases for green plants, namely, GreenPhylDB , Plaza, Phytozome These databases aim to support studies on genomics studies related to plant evolution and to provides comparative data on genomes and gene families and the tools for their analysis.

31. Conti….. It provides information on genomic context of plant genes, Gene homologues, and paralogues, RNA transcripts from the given genes, peptide sequences, and functions of gene families. It allows access to complete genome sequences available in the database.

32. Protein Databases Swiss- Prot Swiss- Prot is a protein sequence and knowledge database. It is well known for high quality of annotation, use of standardized nomenclature, and links to specialized databases. its repository contains the amino acid sequence, the protein name and description, taxonomic data, and citation information PFAM A database of protein families, Pfam contains annotations as well as multiple sequence alignments generated using hidden Markov models

33. Conti… TrEMBL: The European Bioinformatics Institute, collaborating with Swiss- Prot , introduced another database, TrEMBL (translation of EMBL nucleotide sequence database) This database consists of computer annotated entries obtained from the translation of all coding sequences in the nucleotide databases. PIR: The Protein Information Resource (PIR) is an integrated public bioinformatics resource that supports genomic and proteomic research and scientific studies The PIR serves the scientific community through on-line access, and performing off-line sequence identification services for researchers. It is a database of freely accessible protein sequences which contains high-quality data and functional information for the proteins

34. Structure databases There are many structural database that include Protein DataBank (PDB) Important in solving real problems in molecular biology PDB Established in 1972 at Brookhaven National Laboratory (BNL) It contains structural information of the macromolecules determined by X-ray, crystallographic, NMR methods PDB is maintained by the Research Collaboratory for Structural Bioinformatics (RCSB).

35. Conti… PROSITE: is a database of protein domains and families. PROSITE contains biologically significant sites, patterns and profiles that help to reliably identify to which known protein family a new sequence belongs. CATH: The CATH database (Class, architecure , topology, homologous superfamily) is a hierarchical classification of protein domain structures, which clusters proteins at four major structural levels.

36. Pathway databases Pathway databases A pathway database (DB) is a DB that describes biochemical pathways, reactions, and enzymes Some examples of the pathway databases are KEGG (The Kyoto Encyclopedia of Genes and Genomes) BRENDA, Biocyc .

37. Conti… KEGG: The Kyoto Encyclopedia of Genes and Genomes (KEGG) is the primary resource for the Japanese Genome Net service it is a collection of online databases dealing with genomes, enzymatic pathways, and biological chemicals KEGG contains three databases: PATHWAY, GENES, and LIGAND. The PATHWAY database stores computerized knowledge on molecular interaction networks. The GENES database contains data concerning sequences of genes and proteins generated by the genome projects. The LIGAND database holds information about the chemical compounds and chemical reactions that are relevant to cellular processes.

38. BioCyc : The BioCyc Database Collection is a compilation of pathway and genome information for different organisms. It includes two other databases, EcoCyc which describes Escherichia coli K-12; MetaCyc , which describes pathways for more than 300 organisms.