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Bioinformatics Ch1. Introduction 阮雪芬 2002, Oct 17 NTUST www.ntut.edu.tw/~yukijuan/lectures/bioinfo/Oct17.ppt Outline A scenario Life in space and time Dogmas: central and peripheral Observable and data archives Traditional and Current Biology Traditionally, biology has been an observational science. Now, biology has been converted into deductive science. The Data of Bioinformatics Very very large amount Nucleotide sequence databanks contain 16 x 109 bases The full three-dimensional coordinates of proteins of average length ~400 residues: 16000 entries Not only are the individual databanks large, but their sizes are increasing as a very high rate. GenBank Goals “Saw life clearly and saw it whole” Understand integrative aspects of the biology of organisms To interrelate sequence, threedimensional structure, interactions, and function of individual proteins, nucleic acids and protein-nucleic acid complexes Goals To deduce events in evolutionary history. To support application to medicine, agriculture and other scientific fields. A Scenario Imagine a Crisis (1) A new biological virus creates an epidemic of fatal disease in humans Laboratory scientists will or animals isolate its genetic materiala molecule of nucleic acid and determine the sequence. Computer program will then take over Imagine a Crisis (2) Screening this new genome against a data bank of all know genetic messages Developing antiviral therapies: virus contain protein molecules which are suitable targets, for drugs that will interfere with viral structure or function Imagine a Crisis (3) From the viral DNA sequences Computer program Protein sequence Imagine a Crisis (4) From amino acid sequences Computer program Three-dimensional structure Homology Modelling Data bank will be screened for related proteins of know structures Computer program Structure will be predicted A B Ab initio No related protein of known structure is found Ab initio Predicting the structure Design Therapeutic Agents Knowing the viral protein structure Design therapeutic agents Life in space and time In Space Biosphere Ecosystem Darwinian selection or genetic drift Natural mutation The recombination of genes in sexual reproduction Direct gene transfer The generation of variants In Space Ecosystem Species Cell Nuclei, organelles and cytoskeleton Molecules In Time A history of life 3.5 billion years Dogmas: Central and Peripheral Central Dogmas 1957, Crick提出中心教條”DNA製造RNA,RNA 製造蛋白質” 中心教條大體上是對的,但也有些需要修正 有許多RNA病毒:RNADNARNAProtein 跳躍基因 真核細胞RNA需要經過剪接 不只蛋白質具酵素功能,某些RNA也具酵素功能 某些基因可經不同的轉錄起始點或不同的剪接方式, 製備出多種RNA ,而轉錄成功能不同的蛋白質 真核細胞RNA需要經過剪接 不只蛋白質具酵素功能,某些RNA也具 酵素功能 First identified in plant virus Purines and Pyrimidines The Strand in the Double-helix are Antiparalle 3’ 5’ 5’ 3’ Paradigm DNA sequence determines Protein sequence determines Protein structure determines Protein function Most of the organized activity of bioinformatics has been focused on the analysis of the data related to these processes Observable and Data Archives A Databank An archive of information A logical organization Structure of that information Tools to gain access to it A Databank in Molecular Biology Archival databanks of biological information DNA and protein sequence Nucleic acid and protein structure Databanks of protein expression A Databank in Molecular Biology Derived Databanks Sequence motifs Mutations and variants in DNA and protein sequences Classification and relationships Bibliographic Databanks Databanks of web sites Databanks of databanks containing biological information Links between databanks The Mechanism of Access to a Databank is the Set of Tools for answering Question Such as: Does the databank contain the information I require? How can I assemble information from the databank in a useful form? Indices of databanks are useful in asking ” Where can I find some specific piece of information?” A Variety of Possible Kinds of Database Queries Can Arise in Bioinformatics (1) Give a sequence or fragment of a sequence Find sequence in the database that are similar to it A central problem in bioinformatics A Variety of Possible Kinds of Database Queries Can Arise in Bioinformatics (2) Give a protein structure or fragment Find protein structures in the database that are similar to it A Variety of Possible Kinds of Database Queries Can Arise in Bioinformatics (3) Give a sequence of a protein of unknown structure Find structures in the database that adopt similar threedimensional structures A Variety of Possible Kinds of Database Queries Can Arise in Bioinformatics (3) For if two protein have sufficiently similar sequences They will have similar structure A Variety of Possible Kinds of Database Queries Can Arise in Bioinformatics (4) Give a protein structure Find sequences in the data bank that correspond to similar structures A Variety of Possible Kinds of Database Queries Can Arise in Bioinformatics (1) and (2) are solved problems (3) and (4) are active fields of research Curation, Annotation and Quality Control Older data were limited by older techniques Amino acid sequences of protein used to be determined by peptide sequencing. Now, almost al are translated from DNA sequences. Curation, Annotation and Quality Control Distributed error-correction and annotation Dynamic error-correction and annotation