基因與蛋白質資料庫 阮雪芬 nov 20 & 27, 2002 ntu. index genome sequence searching...

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