Lecture 1 Bioinformatics Free Lecture Download

Lecture 1 Bioinformatics Free Lecture Download

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  Dr. Prativa Deka AssociateProfessor Department of Botany Mangaldai College, Mangaldai E-Mail: pdeka.mld@gmail.com Bioinformatics
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  Biologists Collect Molecular Data: DNA& Protein Sequences, Gene Expression, etc. Computer scientists (+Mathematicians, Statisticians, etc.) Develop Tools, Softwares, Algorithms to Store and Analyze the Data. Bioinformaticians Study of Biological Questions by Analyzing Molecular Data Bioinformatics: The field of science in which biology, computer science and information technology merge into a single discipline Paulien hogeweg
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  From DNA toGenome 3 Watson and Crick DNA model Sanger sequences insulin protein Sanger dideoxy DNA sequencing PCR (Polymerase Chain Reaction) 1955 1960 1965 1970 1975 1980 1985 ARPANET (early Internet) PDB (Protein Data Bank) Sequence alignment GenBank database Dayhoff’s Atlas
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  4 1995 1990 2000 SWISS-PROT database NCBI World Wide Web BLAST FASTA EBI HumanGenome Initiative First human genome draft First bacterial genome Yeast genome
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  05/05/2025 5 Biological Databases Whatis a database? – A collection of related data elements • tables • columns (fields) • rows (records) – Records retrieved using a query language – Database technology is well established
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  05/05/2025 6 • Tables(entitites) • basic elements of information to track, e.g., gene, organism, sequence, citation • Columns (fields) • attributes of tables, e.g. for citation table, title, journal, volume, author • Rows (records) • actual data • whereas fields describe what data is stored, the rows of a table are where the actual data is stored
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  05/05/2025 7 How onlinedatabase work? When you query an online database, your query is translated into SQL, the database is interrogated, and the answer displayed on your web browser. Your computer and browser (the “client”) Software to receive and translate the instructions you enter into your browser (on the “server”) The database itself Image source: David Lane and Hugh E. Williams. Web Database Applications with PHP & MySQL. O’Reilly (2002).
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  Why biological databases? •Make biological data available to scientists – Consolidation of data (gather data from different sources) – Provide access to large dataset that cannot be published explicitly (genome, proteome,…) • Make biological data available in computer-readable format – Make data accessible for automated analysis Bioinformatics: “To extract, store and to analysis the biological data”
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  05/05/2025 9 Biological Databases •Over 1000 biological databases • Vary in size, quality, coverage, level of interest • Many of the major ones covered in the annual Database Issue of Nucleic Acids Research • What makes a good database? • comprehensiveness • accuracy • is up-to-date • good interface • batch search/download • API (web services, DAS, etc.)
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  Types of BiologicalDatabases
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  Flow of Databasesin Bioinformatics Biological experiments Biological Databases Computational Biology
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  Plants Genomes Databases PlantGenomes Databases
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  Ten Important BioinformaticsDatabases • GenBank www.ncbi.nlm.nih.gov nucleotide sequences • Ensembl www.ensembl.org human/mouse/Plants genome • PubMed www.ncbi.nlm.nih.gov literature references • NR www.ncbi.nlm.nih.gov protein sequences • SWISS-PROT www.expasy.ch protein sequences • InterPro www.ebi.ac.uk protein domains • OMIM www.ncbi.nlm.nih.gov genetic diseases • Enzymes www.chem.qmul.ac.uk enzymes • PDB www.rcsb.org/pdb/ protein structures • KEGG www.genome.ad.jp metabolic pathways • In 1965, Dayhoff gathered all the available sequence data to create the first bioinformatics database (Atlas of Protein Sequence and Structure).
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  NCBI (National Centerfor Biotechnology Information) •over 30 databases including GenBank, PubMed, OMIM, and GEO • Access all NCBI resources via Entrez (www.ncbi.nlm.nih.gov/Entr ez/)
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  Protein Data Bank(PDB)
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  BLAST For SequenceAlignment • Basic Local Alignment Search Tool – Altschul et al. 1990,1994,1997 • A best method for local alignment • Designed specifically for database searches • Benefits-Speed, User friendly, Statistical rigor, More sensitive • Types of BLAST- BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX
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  Luscombe, Greenbaum, Gerstein(2001)
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  THANK YOU