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

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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

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