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基因與蛋白質資料庫
阮雪芬Nov 20 & 27, 2002
NTU
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
Outline Introduction to genomics Gene Sequence Searching Cutting Site for a Specific Sequence Sequence Alignment Search for Conserved Domains ORF Finding
Genomics
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
mRNA
Proteins
Cell functions
Genome “Genomics”
Proteome“Proteomics”
DNA 和蛋白質合成的地方DNA
Proteins
Sugar Chain
cytoplasm
Genome Gene + Chromosome
Genome
Gene Sequence Searching
Accession Number
Gene Sequence
Gene Sequence SearchingAA046701AA069414AA070289AA446013AA425102
http://www.ncbi.nlm.nih.gov/UniGene/
Gene Sequence Searching
Gene Sequence Searching
Gene Sequence Searching
GGGGGGGGGAAGCTGAGCGCTGAGACCAAGGGCTAAAGCTGGGAGACTGAAAAAATGCAGACCGCCGGGGCATTATTCATTTCTCCAGCTCTGATCCGCTGTTGTACCAGGGGTCTAATCAGGCCTGTGTCTGCCTCCTTCTTGAATAGCCCAGTGAATTCATCTAAACAGCCTTCCTACAGCAACTTCCCACTCCAGGTGGCCAGACGGGAGTTCCAGACCAGTGTTGTCTCCCGGGACATTGACACAGCAGCCAAGTTTATTGGTGCTGGGGCAGCCACAGTTGGTGTGGCTGGTTCAGGGGCTGGCATTGGAACCGTGTTTGGCAGCTTGATCATTGGCTATGCCAGGAACCCGTCTCTCAAGCAGCAGCTCTTCTCCTATGCCATTCTTGGCTTTGCCCTGTCTGAGGCCATGGGGCTTTTCTGTTTGATGGTCGCCTTCCTCATCCTCTTCGCCATGTGAGGCTCCATGGGGGGTCACCGGCCTGTTGCTACTGCAACTCCACACCATTCTTGGTGCTGGGGTGTGTTAAGCTTTACCATTAAACACAACGTTTCTCTAAAAAAAAAAAAAAAAAAAAC
Cutting Site for a Specific Sequence
Sequence
Cut by Restriction Enzymes1. RestrictionMapper2. REBASE3. DARWIN
Cutting Site for a Specific Sequence
RestrictionMapper
http://www.restrictionmapper.org
RestrictionMapper
RestrictionMapper
REBASERebase.neb.com/rebase.html
DARWINhttp://darwin.bio.geneseo.edu/~yin/WebGene/RE.html
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
Pairwise BLAST
BLASTNCBI: 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)
AA046701AA069414AA070289AA446013AA425102
http://gate.sinica.edu.tw:8900/perl/genequery.pl
BGSS
Outline Introduction to proteomics
Primary Structure Analysis
Protein Sequence Searching Protein Sequence Alignment DNA Translate to Protein Protein-protein Interactions
Useful Bio-websites
Proteomics
What Is Proteomics
?
Proteomics Protein +Genome Proteome ProteomeProteomics
How Proteomics Can Help Drug Development
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.
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
Types of Proteomics and Their Applications to Biology
Two-dimensional Gel Approach
Nature 2000, 405, 837-846
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
Primary Structure Analysis
Object: To compute the characters of protein
s. -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
MWpI
Protein Sequence Searching
P02571
Protein Sequence Searching
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
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
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
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
Yeast Protein Linkage Map Data
GeneScape PathwayCalling: Protein interaction and pat
hway Analysis
http://portal.curagen.com
PATHCALLINGYEAST DATABASE
GeneScape
GeneScape
GeneScapeMIPS Currently about 9750 protein-protein-interactions
(8250 physical and 1500 genetic) are annotated.
Yeast Interacting Proteins Database (YIPD)
http://genome.c.kanazawa-u.ac.jp/
Yeast Interacting Proteins Database
Genetic Network Visualization System
Workbench System for Support of Gene Regulatory Network Construction
YIPD
Java Applet
Java Applet
YIPD
GUI SystemHelp
YIPD
Pathway SoftwareBIOCARTA http://biocarta.com/
Browse all pathway
Pathway SoftwareBIOCARTA
Pathway Result 1:Enolase Glycolysis
Pyruvate
Acetyl-CoAethanol lactate
Cancer cells
BIOCARTA
Pathway Result 2:Retinoic Acid Receptor RXR-alpha
BIOCARTA
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