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基因與蛋白質資料庫
阮雪芬Nov 20 & 27, 2002
NTU
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Index Genome
Sequence searching Cutting site for a specifi
c sequence Restriction Mapper REBASE
REBsite NEB cutter v1.0
DARWIN Sequence Alignment
NCBI BLAST Pairwise BLAST
Search for conserved domains
ORF Finder BGSS
Proteome Protein primary structur
e Amino acid and atomic com
position Computing pI and MW
Sequence searching Sequence alignment DNA translate to protein Protein-protein interacti
on on the web YPLMD GeneScape YIPD BIOCARTA
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Outline Introduction to genomics Gene Sequence Searching Cutting Site for a Specific Sequence Sequence Alignment Search for Conserved Domains ORF Finding
Genomics
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Ribose and Deoxyribose
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Backbone of DNA and RNA
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Purines and Pyrimidines
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Watson-Crick Base Pairs
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Watson-Crick Base Pairs
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Watson-Crick Model of Double Helical DNA
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Biochemical Context of Genomics and Proteomics
DNA
mRNA
Proteins
Cell functions
Genome “Genomics”
Proteome“Proteomics”
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DNA 和蛋白質合成的地方DNA
Proteins
Sugar Chain
cytoplasm
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Genome Gene + Chromosome
Genome
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Gene Sequence Searching
Accession Number
Gene Sequence
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Gene Sequence SearchingAA046701AA069414AA070289AA446013AA425102
http://www.ncbi.nlm.nih.gov/UniGene/
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Gene Sequence Searching
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Gene Sequence Searching
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Gene Sequence Searching
GGGGGGGGGAAGCTGAGCGCTGAGACCAAGGGCTAAAGCTGGGAGACTGAAAAAATGCAGACCGCCGGGGCATTATTCATTTCTCCAGCTCTGATCCGCTGTTGTACCAGGGGTCTAATCAGGCCTGTGTCTGCCTCCTTCTTGAATAGCCCAGTGAATTCATCTAAACAGCCTTCCTACAGCAACTTCCCACTCCAGGTGGCCAGACGGGAGTTCCAGACCAGTGTTGTCTCCCGGGACATTGACACAGCAGCCAAGTTTATTGGTGCTGGGGCAGCCACAGTTGGTGTGGCTGGTTCAGGGGCTGGCATTGGAACCGTGTTTGGCAGCTTGATCATTGGCTATGCCAGGAACCCGTCTCTCAAGCAGCAGCTCTTCTCCTATGCCATTCTTGGCTTTGCCCTGTCTGAGGCCATGGGGCTTTTCTGTTTGATGGTCGCCTTCCTCATCCTCTTCGCCATGTGAGGCTCCATGGGGGGTCACCGGCCTGTTGCTACTGCAACTCCACACCATTCTTGGTGCTGGGGTGTGTTAAGCTTTACCATTAAACACAACGTTTCTCTAAAAAAAAAAAAAAAAAAAAC
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Cutting Site for a Specific Sequence
Sequence
Cut by Restriction Enzymes1. RestrictionMapper2. REBASE3. DARWIN
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Cutting Site for a Specific Sequence
RestrictionMapper
http://www.restrictionmapper.org
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RestrictionMapper
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RestrictionMapper
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REBASERebase.neb.com/rebase.html
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DARWINhttp://darwin.bio.geneseo.edu/~yin/WebGene/RE.html
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Sequence Alignment
Input Query
Amino Acid Sequence DNA Sequence
Blastp tblastn blastn blastx tblastx
Compares Against protein Sequence Database
Compares Against Translated Nucleotide Sequence Database
Compares Against Nucleotide Sequence Database
Compares Against protein Sequence Database
Compares Against Translated Nucleotide Sequence Database
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Pairwise BLAST
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BLASTNCBI: http://www.ncbi.nlm.nih.gov/
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Copy Sequence
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Search for Conserved Domains
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ORF Finder (Open Reading Frame Finder)http://www.ncbi.nlm.nih.gov/gorf/
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BGSS(Gene Function Search System)
AA046701AA069414AA070289AA446013AA425102
http://gate.sinica.edu.tw:8900/perl/genequery.pl
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BGSS
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Outline Introduction to proteomics
Primary Structure Analysis
Protein Sequence Searching Protein Sequence Alignment DNA Translate to Protein Protein-protein Interactions
Useful Bio-websites
Proteomics
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What Is Proteomics
?
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Proteomics Protein +Genome Proteome ProteomeProteomics
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How Proteomics Can Help Drug Development
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Definitions of Proteomics First coined in 1995 Be defined as the large-scale
characterization of the entire protein complement of a cell line, tissue, or organism.
Goal: -To obtain a more global and integrated
view of biology by studying all the proteins of a cell rather than each one individually.
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Proteomics Origins In 1975, the introduction of the 2D gel by O’
Farrell who began mapping proteins from E. coli.
The first major technology to emerge for the identification of proteins was the sequencing of proteins by Edman degradationpicomole
MS technology has replaced Edman degradation to identify proteinsfemtomole
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Types of Proteomics and Their Applications to Biology
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Two-dimensional Gel Approach
Nature 2000, 405, 837-846
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Standard Proteome Analysis by 2DE-MS
Current Opinion in Chemical Biology 2000, 4:489–494
Mass Fingerprint Searching in http://www.expasych/tools/peptident.html
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Primary Structure Analysis
Object: To compute the characters of protein
s. -Amino acid composition -Atomic composition -pI -Molecular weight
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Amino Acid & Atomic Composition
ProtParam
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Amino Acid & Atomic Composition
http://www.expasy.ch/tools/protparam.html
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Amino Acid & Atomic Composition
Amino Acid Composition
Atomic Composition
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Computing pI and MW
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Computing pI and MW
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Computing pI and MW
MWpI
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Protein Sequence Searching
P02571
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Protein Sequence Searching
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Sequence AlignmentInput Query
Amino Acid Sequence DNA Sequence
Blastp tblastn blastn blastx tblastx
Compares Against protein Sequence Database
Compares Against Translated Nucleotide Sequence Database
Compares Against Nucleotide Sequence Database
Compares Against protein Sequence Database
Compares Against Translated Nucleotide Sequence Database
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Sequence Alignment
http://www.expasy.ch/
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Sequence Alignment
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Sequence Alignment
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Sequence Alignment
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Sequence Alignment
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Sequence Alignment
Similarity is very low
No similarity
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The Information Stored in Genes Is Expressed by a Multistage Process
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The Genetic Code Is Degenerate
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DNA Translate to Protein
http://www.expasy.ch/tools/
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DNA Translate to Protein
DNA Protein
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DNA Translate to Protein
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DNA Translate to Protein
DNA sequence
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DNA Translate to Protein
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Protein-protein Interactions on the Web
Yeast http://depts.washington.edu/sfields/yplm/data/index.html
http://portal.curagen.com
http://mips.gsf.de/proj/yeast/CYGD/interaction/
http://www.pnas.org/cgi/content/full/97/3/1143/DC1
http://dip.doe-mbi.ucla.edu/
http://genome.c.kanazawa-u.ac.jp/Y2H C. Elegans http://cancerbiology.dfci.harvard.edu/cancerbiology/ResLabs/Vidal/ H. Pylori
http://pim/hybrigenics.com Drosophila
http://gifts.univ-mrs.fr/FlyNets/Flynets_home_page.html
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Yeast Protein Linkage Map Data New protein-protein interactions in yeast
Stanley Fields Lab http://depts.washington.edu/sfields/yplm/data
List of interactions with links to YPD
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Yeast Protein Linkage Map Data
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GeneScape PathwayCalling: Protein interaction and pat
hway Analysis
http://portal.curagen.com
PATHCALLINGYEAST DATABASE
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GeneScape
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GeneScape
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GeneScapeMIPS Currently about 9750 protein-protein-interactions
(8250 physical and 1500 genetic) are annotated.
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Yeast Interacting Proteins Database (YIPD)
http://genome.c.kanazawa-u.ac.jp/
Yeast Interacting Proteins Database
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Genetic Network Visualization System
Workbench System for Support of Gene Regulatory Network Construction
YIPD
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Java Applet
Java Applet
YIPD
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GUI SystemHelp
YIPD
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Pathway SoftwareBIOCARTA http://biocarta.com/
Browse all pathway
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Pathway SoftwareBIOCARTA
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Pathway Result 1:Enolase Glycolysis
Pyruvate
Acetyl-CoAethanol lactate
Cancer cells
BIOCARTA
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Pathway Result 2:Retinoic Acid Receptor RXR-alpha
BIOCARTA
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Useful BioWebSite name URL Information available
MOWSE http://srs.hgmp.mrc.ac.uk/cgi-bin/mowse
Peptide mass mapping and sequencing
ProFound http://prowl.rockefeller.edu/cgi-bin/ProFound
Peptide mass mapping and sequencing
PeptIdent http://www.expasy.ch/tools/peptident. Peptide mass mapping and sequencing
PepSea http://195.41.108.38/PepSeaIntro.html
Peptide mass mapping and sequencing
MASCOT http://www.matrixscience.com/ Peptide mass mapping and sequencing
PepFrag http://www.proteometrics.com/ Peptide mass mapping and sequencing
Protein Prospector
http://prospector.ucsf.edu/ Peptide mass mapping and sequencing
FindMod http://www.expasy.ch/tools/findmod/ Posttranslational modification
SEAQUEST http://fields.scripps.edu/sequest/ Uninterpreted MS/MS searchingFASTA Search Programs
http://fasta.bioch.virginia.edu/ Protein and nucleotide database searching
Cleaved Radioactivity ofPhosphopeptides
http://fasta.bioch.virginia.edu/crp Protein phosphorylation site mapping