RDNA202: Introduction to Bioinformatics Lecture Notes PDF

RDNA202: Introduction to Bioinformatic s Cassie [email protected] Biotechnology and Genomics Lecture 20: Introduction to Bioinformatics Lecture 21 & 22: BLAST and Sequence alignment What is Bioinformatics? The application of computation and analysis tools Goal – t...

RDNA202: Introduction to Bioinformatic s Cassie [email protected] Biotechnology and Genomics Lecture 20: Introduction to Bioinformatics Lecture 21 & 22: BLAST and Sequence alignment What is Bioinformatics? The application of computation and analysis tools Goal – to interpret biological data Involves computer science, biology, physics, chemistry, and statistics techniques to: Deal with problems of biology Understand biological processes Find solutions with information technology to solve biological problems. It is the science of storing, retrieving, and analysing large amounts of biological information What is Bioinformatics? Bioinformatics is an Interdisciplinary Field Science, medicine, and the future: Bioinformatics - PMC (ni  Bioinformatics Used to analyse big Data The human genome – contains about 20 000 protein-coding genes About twice the number of genes as a fruit fly Barely more than a worm Around 12 000 fewer genes than a rice plant But Less than 2 % of the human genome actually encodes proteins The remaining 98% contains: Important regulatory elements Some genes that encode noncoding RNA products instead of proteins Bioinformatics  Bioinformatics – Analyse big Data Techniques designed to identify Transcriptomes – Entire set of RNA molecules produced by a genome Gene expression Proteomes – Structure and properties of every protein produced by a genome  Bioinformatics Centres of Excellence Bioinformatics centers of excellence Found worldwide Responsible for – collecting, cataloguing, and providing open access to published biological data This work began in the early 1980’s When DNA sequence data began to accumulate in scientific literature  Bioinformatics Centres of Excellence Examples: The EMBL-European Bioinformatics Institute (EMBL-EBI) The US National Center for Biotechnology Information (NCBI) The National Institute of Genetics in Japan (NIG) Barcode of Life Data System (BOLD)  Biological Databases These are a collection of data that is: Structured Searchable Periodically updated Cross-referenced Biological Databases - Categories NCBI The National Centre for Biotechnology Information Advances Science and health by providing access to Biomedical and Genomic Information NCBI NCBI – GenBank NCBI – GenBank – What is it? GenBank = NIH genetic sequence database Contains annotated collection of all publicly available DNA sequence Is part of the International Nucleotide Sequence Database Collaboration Comprises: The DNA DataBank of Japan (DDBJ) The European Nucleotide Archive (ENA) GenBank at NCBI Note: these three organisations exchange data on a daily basis GenBank – Information Retrieval  GenBank – Information Retrieval Nucleotide – one of many data selections The nucleotide database = A collection of sequences from several sources – including: GenBank RefSeq TPA PDB Genome, gene, and transcript sequence data Provide the foundation for biomedical research and discovery Lecture 21 & 22: BLAST & Sequence Alignment RDNA202 Cassie [email protected]