Presentation is loading. Please wait.

Presentation is loading. Please wait.

Doug Brutlag 2011 Genome Databases Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University School of Medicine Genomics, Bioinformatics.

Published bySarah Douglas Modified over 9 years ago

Similar presentations

Presentation on theme: "Doug Brutlag 2011 Genome Databases Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University School of Medicine Genomics, Bioinformatics."— Presentation transcript:

1 Doug Brutlag 2011 Genome Databases Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University School of Medicine Genomics, Bioinformatics & Medicine http://biochem158.stanford.edu/

2 Doug Brutlag 2011 Components of a Typical Human GeneGene IntronIntronExonExonExonPromoterTerminator TFBS

3 Doug Brutlag 2011 Active Genes are Transcribed into RNA PrimaryTranscript Gene IntronIntronExon Exon Exon PromoterTerminator

4 Doug Brutlag 2011Transcript mRNA Gene IntronIntronExon Exon Exon PromoterTerminator 5’5’5’5’ 3’3’3’3’ Splicing Splicing Transcript Yields Mature mRNA

5 Doug Brutlag 2011 Mature mRNA contains Coding Region and 5’ and 3’ Untranslated Regions Transcript mRNA Gene IntronIntronExon Exon Exon PromoterTerminator 5’5’5’5’ 3’3’3’3’ Splicing Coding Region 5’UTR 3’UTR 5’UTR 3’UTR

6 Doug Brutlag 2011 Mature mRNA contains 7-Methyl-Guanosine 5’ Cap and 3’ Poly A Tail Transcript mRNA Gene IntronIntronExon Exon Exon PromoterTerminator Splicing Coding Region 5’UTR 3’UTR 5’UTR 3’UTR 7-Me-G-Cap 3’ Poly A Tail

7 Doug Brutlag 2011 ESTs, Full Length cDNA UniGene & RefSeq Databases UniGeneRefSeq Transcript mRNA Gene Intron Exon PromoterTerminator 5’5’ 3’3’ 3’ ESTs 5’ ESTs Full Length cDNA Splicing

8 Doug Brutlag 2011 ESTs, Full Length cDNA UniGene & RefSeq Databases UniGeneRefSeq Transcript mRNA Gene Intron Exon PromoterTerminator 5’5’ 3’3’ 3’ ESTs 5’ ESTs Full Length cDNA Splicing Proteins 5’ UTR 3’ UTR Protein

9 Doug Brutlag 2011 GENSCAN Gene Model http://genes.mit.edu/GENSCAN.html http://genes.mit.edu/GENSCAN.html Hidden Markov models of gene structure

10 Doug Brutlag 2011 Promoters E Additional Data Genomic DNA Assembled contigs A Mapping uniSTS dbSNP Mouse ESTs Human ESTs C Expression Data Entrez Gene Mouse RefSeq Mouse UniGene Human RefSeq Human Ensembl cDNA Genome Databases nrPRO D Protein Similarity pFAM Motifs GrailEXP B Gene Prediction GenScanFGENESH FGENESH+ GeneMark F Summary Entrez Gene UCSC Browser Ensembl

11 Doug Brutlag 2011Inclusive Exon Prediction Entrez Gene Loci http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene NR-Pro Genscan GrailEXP FGENESH Entrez Gene UniGene ESTs

12 Doug Brutlag 2011 Alternative Splicing Generates Distinct Proteins in Different Tissues Transcript mRNA-1 Gene Intron Exon PromoterTerminator 5’5’ 3’3’ Transcript mRNA-2 5’5’3’3’ Alternate Splicing Splicing

13 Doug Brutlag 2011 Alternative Splicing Detected in EST Libraries

14 Doug Brutlag 2011 NCBI Genomes http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome

15 Doug Brutlag 2011 Eukaryote Genome Projects http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi

16 Doug Brutlag 2011 Canis lupus familiaris Genome http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=Retrieve&dopt=Overv iew&list_uids=10726 http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=Retrieve&dopt=Overv iew&list_uids=10726

17 Doug Brutlag 2011 NCBI Entrez Gene http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene

18 Doug Brutlag 2011 NCBI Entrez Gene: Human Opsin http://www.ncbi.nlm.nih.gov/gene?term=human%20opsin http://www.ncbi.nlm.nih.gov/gene?term=human%20opsin

19 Doug Brutlag 2011 Entrez Gene: Human Opsin OPN1MW http://www.ncbi.nlm.nih.gov/gene/2652 http://www.ncbi.nlm.nih.gov/gene/2652

20 Doug Brutlag 2011 Entrez Gene: Human Opsin OPN1MW http://www.ncbi.nlm.nih.gov/gene/2652 http://www.ncbi.nlm.nih.gov/gene/2652

21 Doug Brutlag 2011 MapViewer: Human Opsin OPN1MW http://www.ncbi.nlm.nih.gov/gene/2652 http://www.ncbi.nlm.nih.gov/gene/2652

22 Doug Brutlag 2011 Evidence Viewer for OPN1MW http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&contig=NT_167198.1&gene=OPN1MW& lid=2652&from=4366022&to=4380289 http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&contig=NT_167198.1&gene=OPN1MW& lid=2652&from=4366022&to=4380289

23 Doug Brutlag 2011 OMIM Home Page http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

24 Doug Brutlag 2011 Colorblindness in OMIM

25 Doug Brutlag 2011 Colorblindness in OMIM http://omim.org/entry/303800 http://omim.org/entry/303800

26 Doug Brutlag 2011 Colorblindness in OMIM http://omim.org/entry/303800 http://omim.org/entry/303800

27 Doug Brutlag 2011 Human Genome Resources http://www.ncbi.nlm.nih.gov/genome/guide/human/ http://www.ncbi.nlm.nih.gov/genome/guide/human/

28 Doug Brutlag 2011 RefSeq http://www.ncbi.nlm.nih.gov/RefSeq/ http://www.ncbi.nlm.nih.gov/RefSeq/

29 Doug Brutlag 2011 RefSeq Gene http://www.ncbi.nlm.nih.gov/refseq/rsg/ http://www.ncbi.nlm.nih.gov/refseq/rsg/

30 Doug Brutlag 2011 NCBI UniGene http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene

31 Doug Brutlag 2011 NCBI Homologene Database http://www.ncbi.nlm.nih.gov/homologene http://www.ncbi.nlm.nih.gov/homologene

32 Doug Brutlag 2011 Comparative Genomics

33 Doug Brutlag 2011 Ensembl Home Page http://www.ensembl.org/ http://www.ensembl.org/

34 Doug Brutlag 2011 EBI Genomes Home Page http://www.ensembl.org/ http://www.ensembl.org/

35 Doug Brutlag 2011 Ensembl Human Genome http://www.ensembl.org/Homo_sapiens/ http://www.ensembl.org/Homo_sapiens/

36 Doug Brutlag 2011 Ensembl Human Opsin Search http://uswest.ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;id x=;q=opsin http://uswest.ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;id x=;q=opsin

37 Doug Brutlag 2011 Ensembl Human Opsin Genes http://uswest.ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;id x=;q=opsin http://uswest.ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;id x=;q=opsin

38 Doug Brutlag 2011 Ensembl Human OPN1MW Gene http://uswest.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000 147380;r=X:153448107-153461633 http://uswest.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000 147380;r=X:153448107-153461633

39 Doug Brutlag 2011 Ensembl Opsin OPN1MW Gene Location http://uswest.ensembl.org/Homo_sapiens/Location/View?h=Havana%20gene;r=X:1 53448107-153461633#r=X:153448109-153461632 http://uswest.ensembl.org/Homo_sapiens/Location/View?h=Havana%20gene;r=X:1 53448107-153461633#r=X:153448109-153461632

40 Doug Brutlag 2011 Ensembl OPN1MW Transcripts http://uswest.ensembl.org/Homo_sapiens/Location/View?h=Havana%20gene;r=X:1 53448107-153461633#r=X:153448109-153461632 http://uswest.ensembl.org/Homo_sapiens/Location/View?h=Havana%20gene;r=X:1 53448107-153461633#r=X:153448109-153461632

41 Doug Brutlag 2011 Ensembl OPN1MW Opsin Protein http://uswest.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000 147380;r=X:153448107-153461633;t=ENST00000369935 http://uswest.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000 147380;r=X:153448107-153461633;t=ENST00000369935

42 Doug Brutlag 2011 Ensembl Tutorials http://uswest.ensembl.org/info/website/tutorials/index.html http://uswest.ensembl.org/info/website/tutorials/index.html

43 Doug Brutlag 2011 UCSC Genome Home Page http://genome.ucsc.edu/ http://genome.ucsc.edu/

44 Doug Brutlag 2011 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgGateway http://genome.ucsc.edu/cgi-bin/hgGateway

45 Doug Brutlag 2011 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgGateway http://genome.ucsc.edu/cgi-bin/hgGateway

46 Doug Brutlag 2011 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:153485203- 153499469&hgsid=216983641&knownGene=pack&hgFind.matches=uc004fkd.2, http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:153485203- 153499469&hgsid=216983641&knownGene=pack&hgFind.matches=uc004fkd.2,

47 Doug Brutlag 2011 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:153485203- 153499469&hgsid=216983641&knownGene=pack&hgFind.matches=uc004fkd.2, http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:153485203- 153499469&hgsid=216983641&knownGene=pack&hgFind.matches=uc004fkd.2,

48 Doug Brutlag 2011 UCSC Proteome Browser http://genome.ucsc.edu/cgi-bin/pbGateway http://genome.ucsc.edu/cgi-bin/pbGateway

49 Doug Brutlag 2011 UCSC Proteome Browser http://genome.ucsc.edu/cgi-bin/pbGateway http://genome.ucsc.edu/cgi-bin/pbGateway

50 Doug Brutlag 2011 UCSC Help File http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html

Download ppt "Doug Brutlag 2011 Genome Databases Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University School of Medicine Genomics, Bioinformatics."

Similar presentations

Ch 17 Gene Expression I: Transcription

Ch 17 Gene Expression I: Transcription
Peter Tsai, Bioinformatics Institute.  University of California, Santa Cruz (UCSC)  A rapid and reliable display of any requested portion of genomes.

Peter Tsai, Bioinformatics Institute.  University of California, Santa Cruz (UCSC)  A rapid and reliable display of any requested portion of genomes.
1 Computational Molecular Biology MPI for Molecular Genetics DNA sequence analysis Gene prediction Gene prediction methods Gene indices Mapping cDNA on.

1 Computational Molecular Biology MPI for Molecular Genetics DNA sequence analysis Gene prediction Gene prediction methods Gene indices Mapping cDNA on.
Visualization of genomic data Genome browsers. UCSC browser Ensembl browser Others ? Survey.

Visualization of genomic data Genome browsers. UCSC browser Ensembl browser Others ? Survey.
Tutorial 7 Genome browser. Free, open source, on-line broswer for genomes Contains ~100 genomes, from nematodes to human. Many tools that can be used.

Tutorial 7 Genome browser. Free, open source, on-line broswer for genomes Contains ~100 genomes, from nematodes to human. Many tools that can be used.
Genome Browsers Carsten O. Daub Omics Science Center RIKEN, Japan May 2008.

Genome Browsers Carsten O. Daub Omics Science Center RIKEN, Japan May 2008.
Gene Expression And Regulation Bioinformatics January 11, 2006 D. A. McClellan

Gene Expression And Regulation Bioinformatics January 11, 2006 D. A. McClellan
Sequence Analysis MUPGRET June workshops. Today What can you do with the sequence? What can you do with the ESTs? The case of SNP and Indel.

Sequence Analysis MUPGRET June workshops. Today What can you do with the sequence? What can you do with the ESTs? The case of SNP and Indel.
Alignment of mRNAs to genomic DNA Sequence Martin Berglund Khanh Huy Bui Md. Asaduzzaman Jean-Luc Leblond.

Alignment of mRNAs to genomic DNA Sequence Martin Berglund Khanh Huy Bui Md. Asaduzzaman Jean-Luc Leblond.
Genome Related Biological Databases. Content DNA Sequence databases Protein databases Gene prediction Accession numbers NCBI website Ensembl website.

Genome Related Biological Databases. Content DNA Sequence databases Protein databases Gene prediction Accession numbers NCBI website Ensembl website.
Genomic Database - Ensembl Ka-Lok Ng Department of Bioinformatics Asia University.

Genomic Database - Ensembl Ka-Lok Ng Department of Bioinformatics Asia University.
Sequence Analysis. Today How to retrieve a DNA sequence? How to search for other related DNA sequences? How to search for its protein sequence? How to.

Sequence Analysis. Today How to retrieve a DNA sequence? How to search for other related DNA sequences? How to search for its protein sequence? How to.
Computational Molecular Biology Biochem 218 – BioMedical Informatics 231 Gene Regulatory.

Computational Molecular Biology Biochem 218 – BioMedical Informatics Gene Regulatory.
Doug Brutlag Professor Emeritus Biochemistry & Medicine (by courtesy) Genome Databases Computational Molecular Biology Biochem 218 – BioMedical Informatics.

Doug Brutlag Professor Emeritus Biochemistry & Medicine (by courtesy) Genome Databases Computational Molecular Biology Biochem 218 – BioMedical Informatics.
Doug Brutlag 2011 Next Generation Sequencing and Human Genome Databases Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University.

Doug Brutlag 2011 Next Generation Sequencing and Human Genome Databases Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University.
On line (DNA and amino acid) Sequence Information

On line (DNA and amino acid) Sequence Information
Databases in Bioinformatics and Systems Biology Carsten O. Daub Omics Science Center RIKEN, Japan May 2008.

Databases in Bioinformatics and Systems Biology Carsten O. Daub Omics Science Center RIKEN, Japan May 2008.
Genome Annotation BBSI July 14, 2005 Rita Shiang.

Genome Annotation BBSI July 14, 2005 Rita Shiang.
UCSC Genome Browser 1. The Progress 2 Database and Tool Explosion 3 2000 : 230 databases and tools 1996 : first annual compilation of databases and tools.

UCSC Genome Browser 1. The Progress 2 Database and Tool Explosion : 230 databases and tools 1996 : first annual compilation of databases and tools.
Professional Development Course 1 – Molecular Medicine Genome Biology June 12, 2012 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services.

Professional Development Course 1 – Molecular Medicine Genome Biology June 12, 2012 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services.

Similar presentations

Ads by Google