BIOINFORMATICS AND DATABASES IN BIOINFORMATICS.pdf

BIOINFORMATICS AND DATABASES IN BIOINFORMATICS.pdf

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  Dr. Harisingh GourViswavidyalaya A Central University DEPARTMENT OF ZOOLOGY TOPIC – DATABASES IN BIOINFORMATICS MID II ASSIGNMENT ZOO – SEC – 128 SUBMITED TO – MR. ANUPAM KUMAR SUBMITED BY – PRAVANJAN DASH ROLL NO. – Y23265020, Msc 1st YEAR, 1st SEMESTER
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  INTRODUCTION OF DATABASE BIOLOGICALDATABASES are  Collection of files containing records of biological data in machine readable form Can be accessed, added, retrieved, manipulated and modified.  Store, manage, connect and distribute data.  Data are arranged by sets of rules which are programmed into software that manages the data called Database Management System or DBMS.  A biological database is a collection of data that is structured, searchable, updated periodically and cross referenced.  The data is stores, maintained, annotated, curated and stored for public/research use.  Data collected and organized in a specific but useful way
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  Classification based ontype of data stored  Primary Databases: Contain original data in the form of primary sequence data or structural data as submitted by the scientific community.  Secondary Databases: Contain information that has been processed and derived from the raw data available in primary database.eg: PROSITE, PRINTS, BLOCKS etc..  Composite Databases: Collect and present data after comparing and filtering them from different primary databases and exhibit only the non redundant sequences.
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  PRIMARY DATA VERSUSSECONDARY DATA PRIMARY DATA • Primary data is a type of data researchers directly collect from main sources. • Includes real-time data. • Collected to address a current research problem. • Accessing primary data includes a relatively long process. • Data collection tools include observations, surveys, questionnaires, physical testing, online questionnaires, personal or telephone interviews, case studies, and focused group discussions. SECONDARY DATA • Secondary data refers to already existing data produced by the previous researchers. • Related to the past. • Primarily collected to address previously existed research problems and can be used to address the current research problem as well. • Referring to secondary data is quick and easy. • Data collection tools include journal articles, websites, books, government publications, records, etc.
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  PRIMARY DATABASES  Primarydatabases contain original biological data. They are archives of raw sequence or structural data submitted by the scientific community.  Once given a database a accession number, the data in primary database are never changed.  There are three (Genbank, EMBL, DDBJ) major public sequence databases that store raw nucleic acid sequence data produced and submitted by researchers worldwide.  SOME PRIMARY DATABASES Nucleic acid databases: Gen Bank, EMBL, DDBJ Protein sequence databases: PIR, Swiss-Prot, UNIPROT Protein structure database: PDB Metabolic databases: KEGG
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  SECONDARY DATABASE • Secondarydatabase contain additional information derived from the analysis f data available in primary sources. econdary databases are analysed in a variety Of ways and contain different formation in different formats. • SOME SECONDARY DATABASES ARE  TrEMBL  Pfam  PROSITE  Profiles  SCOP  CATH
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  NUCLEOTIDE SEQUENCE DATABASE •Composed of a group of nucleotide sequence entries. • Data repositories that accept nucleic acid sequence data and make it freely available to the public. • All the three are members of the International Nucleotide Sequence Database Consortium (INSDC) and interchange data. • GenBank, EMBL, DDBJ are principal nucleotide databases.
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  PROTEIN SEQUENCE DATABASES An array of amino acid sequence entries arranged according to the identification number.  Well known protein sequence databases available on www are  Swiss-Prot  PIR  UNIPROT
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  PROTEIN STRUCTURE DATABASE Many proteins which exhibit a common evolutionary origin, show structural similarities.  Dissimilar proteins exhibit changes in primary, secondary, teritiary and quarternary structures.  Similar or dissimilar protein structure can be predicted with structure database.  These databases store a collection of three dimensional structures of proteins.  EXAMPLE IS pluggable database (PDB) .
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  THANK YOU