Download Proteome

基因與蛋白質資料庫
阮雪芬
Nov 20 & 27, 2002
NTU
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Genome
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Sequence searching
Cutting site for a
specific sequence
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Restriction Mapper
REBASE
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REBsite
NEB cutter v1.0
DARWIN
Sequence Alignment
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Index
NCBI
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BLAST
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Pairwise BLAST
Search for conserved
domains
ORF Finder
BGSS
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Proteome
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Protein primary
structure
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Amino acid and atomic
composition
Computing pI and MW
Sequence searching
Sequence alignment
DNA translate to
protein
Protein-protein
interaction on the web
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YPLMD
GeneScape
YIPD
BIOCARTA
Outline
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Introduction to genomics
Gene Sequence Searching
Cutting Site for a Specific Sequence
Sequence Alignment
Search for Conserved Domains
ORF Finding
Ribose and Deoxyribose
Backbone of DNA and RNA
Purines and Pyrimidines
Watson-Crick Base Pairs
Watson-Crick Base Pairs
Watson-Crick Model of Double
Helical DNA
Biochemical Context of
Genomics and Proteomics
DNA
Genome
“Genomics”
mRNA
Proteins
Cell functions
Proteome
“Proteomics”
DNA 和蛋白質合成的地方
DNA
Proteins
Sugar Chain
cytoplasm
Genome
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Gene
+ Chromosome
Genome
Gene Sequence Searching
Accession Number
Gene Sequence
Gene Sequence Searching
AA046701
AA069414
AA070289
AA446013
AA425102
http://www.ncbi.nlm.nih.gov/UniGene/
Gene Sequence Searching
Gene Sequence Searching
Gene Sequence Searching
GGGGGGGGGAAGCTGAGCGCTGAGACCAAGGGCTAAAGCTGGGAGACTGAAAAAATGCAG
ACCGCCGGGGCATTATTCATTTCTCCAGCTCTGATCCGCTGTTGTACCAGGGGTCTAATC
AGGCCTGTGTCTGCCTCCTTCTTGAATAGCCCAGTGAATTCATCTAAACAGCCTTCCTAC
AGCAACTTCCCACTCCAGGTGGCCAGACGGGAGTTCCAGACCAGTGTTGTCTCCCGGGAC
ATTGACACAGCAGCCAAGTTTATTGGTGCTGGGGCAGCCACAGTTGGTGTGGCTGGTTCA
GGGGCTGGCATTGGAACCGTGTTTGGCAGCTTGATCATTGGCTATGCCAGGAACCCGTCT
CTCAAGCAGCAGCTCTTCTCCTATGCCATTCTTGGCTTTGCCCTGTCTGAGGCCATGGGG
CTTTTCTGTTTGATGGTCGCCTTCCTCATCCTCTTCGCCATGTGAGGCTCCATGGGGGGT
CACCGGCCTGTTGCTACTGCAACTCCACACCATTCTTGGTGCTGGGGTGTGTTAAGCTTT
ACCATTAAACACAACGTTTCTCTAAAAAAAAAAAAAAAAAAAAC
Cutting Site for a Specific
Sequence
Sequence
Cut by Restriction Enzymes
1. RestrictionMapper
2. REBASE
3. DARWIN
Cutting Site for a Specific
Sequence
RestrictionMapper
http://www.restrictionmapper.org
RestrictionMapper
RestrictionMapper
REBASE
Rebase.neb.com/rebase.html
DARWIN
http://darwin.bio.geneseo.edu/~yin/WebGene/
RE.html
Sequence Alignment
Input Query
DNA Sequence
Amino Acid Sequence
Blastp
Compares
Against
protein
Sequence
Database
tblastn
Compares
Against
Translated
Nucleotide
Sequence
Database
blastn
Compares
Against
Nucleotide
Sequence
Database
blastx
tblastx
Compares
Against
protein
Sequence
Database
Compares
Against
Translated
Nucleotide
Sequence
Database
Pairwise BLAST
BLAST
NCBI:
http://www.ncbi.nlm.nih.gov/
Copy Sequence
Search for Conserved
Domains
ORF Finder
(Open Reading Frame Finder)
http://www.ncbi.nlm.nih.gov/gorf/
BGSS
(Gene Function Search System)
AA046701
AA069414
AA070289
AA446013
AA425102
http://gate.sinica.edu.tw:8900/perl/genequery.pl
BGSS
Outline
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Introduction to proteomics
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Primary Structure Analysis
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Protein Sequence Searching
Protein Sequence Alignment
DNA Translate to Protein
Protein-protein Interactions
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Useful Bio-websites
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What Is Proteomics
?
Proteomics
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Protein +Genome Proteome
ProteomeProteomics
How Proteomics Can Help
Drug Development
Definitions of Proteomics
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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.
Proteomics Origins
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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
degradationpicomole
MS technology has replaced Edman
degradation to identify proteinsfemtomole
Types of Proteomics and
Their Applications to Biology
Two-dimensional Gel Approach
Nature 2000, 405, 837-846
Standard Proteome Analysis
by 2DE-MS
Mass Fingerprint
Searching in
http://www.expas
ych/tools/peptide
nt.html
Current Opinion in
Chemical Biology 2000,
4:489–494
Primary Structure Analysis
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Object:
To compute the characters of
proteins.
-Amino acid composition
-Atomic composition
-pI
-Molecular weight
Amino Acid & Atomic Composition
ProtParam
Amino Acid & Atomic Composition
http://www.expasy.ch/tools/protparam.html
Amino Acid & Atomic Composition
Amino Acid Composition
Atomic Composition
Computing pI and MW
Computing pI and MW
Computing pI and MW
MW
pI
Protein Sequence Searching
P02571
Protein Sequence Searching
Sequence Alignment
Input Query
DNA Sequence
Amino Acid Sequence
Blastp
Compares
Against
protein
Sequence
Database
tblastn
Compares
Against
Translated
Nucleotide
Sequence
Database
blastn
Compares
Against
Nucleotide
Sequence
Database
blastx
tblastx
Compares
Against
protein
Sequence
Database
Compares
Against
Translated
Nucleotide
Sequence
Database
Sequence Alignment
http://www.expasy.ch/
Sequence Alignment
Sequence Alignment
Sequence Alignment
Sequence Alignment
Sequence Alignment
Similarity is very low
No similarity
The Information Stored in Genes Is
Expressed by a Multistage Process
The Genetic Code Is Degenerate
DNA Translate to Protein
http://www.expasy.ch/tools/
DNA Translate to Protein
DNA
Protein
DNA Translate to Protein
DNA Translate to Protein
DNA sequence
DNA Translate to Protein
Protein-protein Interactions on
the Web
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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
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C. Elegans
http://cancerbiology.dfci.harvard.edu/cancerbiology/ResLabs/Vidal/
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H. Pylori
http://pim/hybrigenics.com
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Drosophila
http://gifts.univ-mrs.fr/FlyNets/Flynets_home_page.html
Yeast Protein Linkage Map Data
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New protein-protein interactions in yeast
List of
interactions with
links to YPD
Stanley Fields Lab
http://depts.washington.edu/sfields/yplm/data
Yeast Protein Linkage Map Data
GeneScape
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PathwayCalling: Protein interaction and
pathway Analysis
PATHCALLING
YEAST DATABASE
http://portal.curagen.com
GeneScape
GeneScape
GeneScapeMIPS
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Currently about 9750 protein-protein-interactions
(8250 physical and 1500 genetic) are annotated.
Yeast Interacting Proteins
Database (YIPD)
Yeast
Interacting
Proteins
Database
http://genome.c.kanazawa-u.ac.jp/
Genetic Network Visualization
System
Workbench System for Support of Gene Regulatory Network Construction
Java Applet
Java Applet
GUI System
Help
Pathway Software
BIOCARTA
http://biocarta.com/
Browse all pathway
Pathway Software
BIOCARTA
Pathway Result 1:
Enolase
Pyruvate
Cancer cells
Acetyl-CoA ethanol
lactate
Glycolysis
Pathway Result 2:
Retinoic Acid Receptor RXR-alpha
Useful BioWeb
Site name
URL
Information available
MOWSE
http://srs.hgmp.mrc.ac.uk/cgi-bin/mowse
Peptide mass mapping and sequencing
ProFound
http://prowl.rockefeller.edu/cgibin/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 searching
FASTA Search
Programs
http://fasta.bioch.virginia.edu/
Protein and nucleotide database
searching
Cleaved
Radioactivity of
http://fasta.bioch.virginia.edu/crp
Protein phosphorylation site mapping