The Introduction of BIOINFORMATICS etc.pdf

The Introduction of BIOINFORMATICS etc.pdf

• 1.
  BIOINFORMATICS Introduction
• 2.
  MK Bioinformatika –1 sks • Kuliah berupa praktikum, dilaksanakan di lab komputer • Dibagi 2 kelas, bergantian masuk kelas dan tugas mandiri tiap minggu • Dilarang berpindah kelas kecuali ada ijin khusus (sakit/tugas) • Nilai: tugas mandiri & ukd • Tugas dikumpulkan dalam CD sesuai waktu yang telah ditentukan. 1 CD Per tugas per anak
• 3.
  Topik dlm MKBioinformatika • Pengenalan Bioinformatika dan Penyedia layanan bioinformatika (NCBI & EBI) • Database Biologi • Pairwise sequence alignment & database similarity searching (BLAST) • Multiple sequences alignment (CLUSTAL) • UKD
• 4.
  • Gene andpromoter prediction • Primer design • Molecular phylogenetics & phylogenetic tree construction • Structural Bioinformatics • UKD
• 5.
  Reference/text book • EssentialBioinformatics (Jin Xiong) • Bioinformatics for dummies (Claverie & Notredame)
• 6.
  biological research mathematical, statistical, or computationaltools synthesize recorded data and integrate various types of information in the process of answering a particular biological question GregorMendel and ThomasMorgan : by simply counting genetic variations of plants and fruit flies, were able to discover the principles of genetic inheritance using calculus to predict the growth rate of a human population or to establish a kinetic model for enzyme catalysis
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  Biological experiments • Invivo: within a living organism • In vitro: in an artificial environment • In silico: bioinformatics
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  Bioinformatics the disciplineof quantitative analysis of information relating to biological macromolecules with the aid of Computers : the technology that uses computers for storage, retrieval, manipulation, and distribution of information related to biological macromolecules such as DNA, RNA, and proteins The development of bioinformatics as a field is the result of advances in both molecular biology and computer science over the past 30–40 years the use of computers because most of the tasks in genomic data analysis are highly repetitive or mathematically complex computer science biological science bioinformatics
• 9.
  History • Margaret Dayhoffin 1965: developed a first protein sequence database called Atlas of Protein Sequence and Structure • 1970s : the Brookhaven National Laboratory established the Protein Data Bank for archiving three-dimensional protein structures • The first sequence alignment algorithm was developed by Needleman and Wunsch in 1970 • The first protein structure prediction algorithm was developed by Chou and Fasman in 1974 • The 1980s : the establishment of GenBank and the development of fast database searching algorithms such as FASTA by William Pearson and BLAST by Stephen Altschul and coworkers • The start of the human genome project in the late 1980s provided a major boost for the development of bioinformatics. • The development and the increasingly widespread use of the Internet in the 1990s made instant access to, and exchange and dissemination of, biological data possible
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  • Bioinformatics differsfrom a related field known as computational biology. • Bioinformatics is limited to sequence, structural, and functional analysis of genes and genomes and their corresponding products and is often considered computational molecular biology. • However, computational biology encompasses all biological areas that involve computation. For example, mathematical modeling of ecosystems, population dynamics, application of the game theory in behavioral studies, and phylogenetic construction using fossil records all employ computational tools, but do not necessarily involve biological macromolecules
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  to better understanda living cell and how it functions at the molecular level the flow of genetic information is dictated by the “central dogma” of biology in which DNA is transcribed to RNA, which is translated to proteins. Cellular functions are mainly performed by proteins whose capabilities are ultimately determined by their sequences The ultimate goal of bioinformatics Bioinformatics consists of two subfields: The development of computational tools and databases The application of these tools and databases in generating biological knowledge
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  The tool development •writing software for sequence, structural, and functional analysis • the construction and curating of biological databases Molecular functional analysis Molecular sequence analysis Molecular structural analysis
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  APPLICATIONS • Basic genomicand molecular biology research • Biotechnology and biomedical sciences • Knowledge-based drug design Computational studies of protein–ligand interactions provide a rational basis for the rapid identification of novel leads for synthetic drugs. Knowledge of the three-dimensional structures of proteins allows molecules to be designed that are capable of binding to the receptor site of a target protein with great affinity and specificity Significantly reduces the time and cost necessary to develop drugs with higher potency, fewer side effects, and less toxicity than using the traditional trial-and-error approach
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  • Forensic DNAanalysis • Agricultural biotechnology results from molecular phylogenetic analysis have been accepted as evidence in criminal courts Plant genome databases and gene expression profile analyses have played an important role in the development of new crop varieties that have higher productivity and more resistance to disease
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  Bioinformatics Paradigm • Findthe data • Download the data • Reformat the data • Collect the samples • Run molecular analysis • Filter the data • Run analysis software • Collect and sort results • Publish / Data sharing
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  Penyedia Layanan Bioinformatika
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  Layanan dasar • Database: nucleotide & protein sequences, human genome, genetic diseases, enzymes, protein structure, metabolic pathways • Tools bioinformatika : analisis sekuens DNA/RNA dan protein, homology, database search, PCR primers design, restriction map, structure prediction, tree reconstruction • Literature references
• 19.
  Beberapa database bioinformatika •GenBank/DDBJ/EMBL : sekuens nukleotida (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide) • Ensembl : human/mouse genome (www.ensembl.org) • PubMed : literature references (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed) • Swiss-Prot : sekuens protein (www.expasy.ch) • interPro : protein domains (www.ebi.ac.uk) • Enzymes (www.chem.qmul.ac.uk) • PDB : struktur protein (www.rscb.org/pdb/) • KEGG : metabolic pathways (www.genome.ad.jp)
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  Beberapa software bioinformatika gratis •Data base search : SRS, Entrez, BLAST, DALI • Multiple alignment : ClustalW, MUSCLE, Tcoffee • Prediction : GenScan, PsiPred, Mfold • Phylogenetics : Phylip, PhyML • Edition/Visualization : Jalview, Trees, Rasmol
• 21.
  Penyedia layanan bioinformatika utama •NCBI : National Center for Biotechnology Information (www.ncbi.nlm.nih.gov) • EBI : European Bioinformatics Institute (www.ebi.ac.uk)
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  Tugas • Buka websiteNCBI dan EBI, eksplorasi, dan sebutkan apa saja yang dapat anda manfaatkan di situ. • Tuliskan topik penelitian yang akan anda teliti lalu Cari literatur terkini yang terkait dengan penelitian anda. Gunakan database pubmed di NCBI. Pilih sepuluh referensi yang paling relevan dan terkini, simpan abstraknya.