Bioinformatics Ch1. Introduction 阮阮阮 2002, Oct 17 NTUST ww.ntut.edu.tw/~yukijuan/lectures/bioinfo/Oct17.ppt
Welcome message from author
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
BioinformaticsCh1. Introduction
阮雪芬2002, Oct 17NTUST
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”
To interrelate sequence, three-dimensional structure, interactions, and function of individual proteins, nucleic acids and protein-nucleic acid complexes
Understand integrative aspects of the biology of organisms
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 or animals Laboratory scientists will
isolate its genetic material-a 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
Protein sequence
Computer program
Imagine a Crisis (4)
From amino acid sequences
Three-dimensional structure
Computer program
Homology Modelling
Data bank will be screened for related proteins of know structures
Structure will be predicted
AB
Computer program
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
5’ 3’
3’
5’
Paradigm
DNA sequence
Protein sequence
Protein structure
Protein function
determines
determines
determines
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?”
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 (1)
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 (2)
Give a sequence of a protein of unknown structure
Find structures in the database that adopt similar three-dimensional structures
A Variety of Possible Kinds of Database Queries Can Arise in Bioinformatics (3)
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
Related Documents
