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Next Generation Sequencing and Human Genome Databases
Next Generation Sequencing and Human Genome Databases
Illumina Solexa Sequencing Technology
Illumina Solexa Sequencing Technology
Emulsion Based Clonal Amplification
Emulsion Based Clonal Amplification
Pacific Biosciences SMRT Sequencing
Pacific Biosciences SMRT Sequencing
Pacific Biosciences Sequencing
Pacific Biosciences Sequencing
Phospholinked Fluorophores
Phospholinked Fluorophores
Processive Synthesis
Processive Synthesis
Synthesis of Long Duplex DNA
Synthesis of Long Duplex DNA
Highly Parallel Optics System
Highly Parallel Optics System
Circular Templates Gives Redundant Sequencing and Accuracy
Circular Templates Gives Redundant Sequencing and Accuracy
Circular Templates Gives Redundant Sequencing and Accuracy
Circular Templates Gives Redundant Sequencing and Accuracy
Ion Torrent Sequencing
Ion Torrent Sequencing
Ion Torrent Sequencing
Ion Torrent Sequencing
Ion Torrent Sequencing
Ion Torrent Sequencing
The Human Genome How fast is the cost going down
The Human Genome How fast is the cost going down
Archon Genomics X-Prize
Archon Genomics X-Prize
Archon Genomics X-Prize
Archon Genomics X-Prize
Components of a Typical Human Gene
Components of a Typical Human Gene
Active Genes are Transcribed into RNA
Active Genes are Transcribed into RNA
Splicing Transcript Yields Mature mRNA
Splicing Transcript Yields Mature mRNA
Mature mRNA contains Coding Region and 5’ and 3’ Untranslated Regions
Mature mRNA contains Coding Region and 5’ and 3’ Untranslated Regions
Mature mRNA contains 7-Methyl-Guanosine 5’ Cap and 3’ Poly A Tail
Mature mRNA contains 7-Methyl-Guanosine 5’ Cap and 3’ Poly A Tail
ESTs, Full Length cDNA UniGene & RefSeq Databases
ESTs, Full Length cDNA UniGene & RefSeq Databases
ESTs, Full Length cDNA UniGene & RefSeq Databases
ESTs, Full Length cDNA UniGene & RefSeq Databases
GENSCAN Gene Model http://genes
GENSCAN Gene Model http://genes
Genome Databases
Genome Databases
Entrez Gene Loci http://www
Entrez Gene Loci http://www
Alternative Splicing Generates Distinct Proteins in Different Tissues
Alternative Splicing Generates Distinct Proteins in Different Tissues
Alternative Splicing Detected in EST Libraries
Alternative Splicing Detected in EST Libraries
NCBI Genomes http://www
NCBI Genomes http://www
Eukaryote Genome Projects http://www
Eukaryote Genome Projects http://www
Canis lupus familiaris Genome http://www
Canis lupus familiaris Genome http://www
NCBI Entrez Gene http://www
NCBI Entrez Gene http://www
NCBI Entrez Gene: Human Opsin http://www
NCBI Entrez Gene: Human Opsin http://www
Entrez Gene: Human Opsin OPN1MW http://www
Entrez Gene: Human Opsin OPN1MW http://www
Entrez Gene: Human Opsin OPN1MW http://www
Entrez Gene: Human Opsin OPN1MW http://www
MapViewer: Human Opsin OPN1MW http://www
MapViewer: Human Opsin OPN1MW http://www
Evidence Viewer for OPN1MW http://www
Evidence Viewer for OPN1MW http://www
OMIM Home Page http://www
OMIM Home Page http://www
Colorblindness in OMIM
Colorblindness in OMIM
Colorblindness in OMIM http://omim
Colorblindness in OMIM http://omim
Human Genome Resources http://www
Human Genome Resources http://www
RefSeq http://www
RefSeq http://www
RefSeq Gene http://www
RefSeq Gene http://www
NCBI UniGene http://www
NCBI UniGene http://www
NCBI Homologene Database http://www
NCBI Homologene Database http://www
Comparative Genomics
Comparative Genomics
Ensembl Home Page http://www
Ensembl Home Page http://www
EBI Genomes Home Page http://www
EBI Genomes Home Page http://www
Ensembl Human Genome http://www
Ensembl Human Genome http://www
Ensembl Human Opsin Search http://uswest
Ensembl Human Opsin Search http://uswest
Ensembl Human Opsin Genes http://uswest
Ensembl Human Opsin Genes http://uswest
Ensembl Human OPN1MW Gene http://uswest
Ensembl Human OPN1MW Gene http://uswest
Ensembl Opsin OPN1MW Gene Location http://uswest
Ensembl Opsin OPN1MW Gene Location http://uswest
Ensembl OPN1MW Transcripts http://uswest
Ensembl OPN1MW Transcripts http://uswest
Ensembl OPN1MW Opsin Protein http://uswest
Ensembl OPN1MW Opsin Protein http://uswest
Ensembl Tutorials http://uswest
Ensembl Tutorials http://uswest
UCSC Genome Home Page http://genome
UCSC Genome Home Page http://genome
UCSC Genome Browser http://genome
UCSC Genome Browser http://genome
UCSC Genome Browser http://genome
UCSC Genome Browser http://genome
UCSC Genome Browser http://genome
UCSC Genome Browser http://genome
UCSC Genome Browser http://genome
UCSC Genome Browser http://genome
UCSC Proteome Browser http://genome
UCSC Proteome Browser http://genome
UCSC Proteome Browser http://genome
UCSC Proteome Browser http://genome
UCSC Help File http://genome
UCSC Help File http://genome

Презентация: «Next Generation Sequencing and Human Genome Databases». Автор: Doug Brutlag. Файл: «Next Generation Sequencing and Human Genome Databases.ppt». Размер zip-архива: 8920 КБ.

Next Generation Sequencing and Human Genome Databases

содержание презентации «Next Generation Sequencing and Human Genome Databases.ppt»
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1 Next Generation Sequencing and Human Genome Databases

Next Generation Sequencing and Human Genome Databases

Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University School of Medicine

Genomics, Bioinformatics & Medicine http://biochem158.stanford.edu/

2 Illumina Solexa Sequencing Technology

Illumina Solexa Sequencing Technology

3 Emulsion Based Clonal Amplification

Emulsion Based Clonal Amplification

4 Pacific Biosciences SMRT Sequencing

Pacific Biosciences SMRT Sequencing

5 Pacific Biosciences Sequencing

Pacific Biosciences Sequencing

6 Phospholinked Fluorophores

Phospholinked Fluorophores

7 Processive Synthesis

Processive Synthesis

8 Synthesis of Long Duplex DNA

Synthesis of Long Duplex DNA

9 Highly Parallel Optics System

Highly Parallel Optics System

10 Circular Templates Gives Redundant Sequencing and Accuracy

Circular Templates Gives Redundant Sequencing and Accuracy

11 Circular Templates Gives Redundant Sequencing and Accuracy

Circular Templates Gives Redundant Sequencing and Accuracy

12 Ion Torrent Sequencing

Ion Torrent Sequencing

13 Ion Torrent Sequencing

Ion Torrent Sequencing

14 Ion Torrent Sequencing

Ion Torrent Sequencing

15 The Human Genome How fast is the cost going down

The Human Genome How fast is the cost going down

2006: $ 50 million 2008: $500,000 2009: $50,000 2010: $20,000 2011: $5,000 2012:??? $1,000

Thanks to Serafim Batzoglou

16 Archon Genomics X-Prize

Archon Genomics X-Prize

17 Archon Genomics X-Prize

Archon Genomics X-Prize

18 Components of a Typical Human Gene

Components of a Typical Human Gene

19 Active Genes are Transcribed into RNA

Active Genes are Transcribed into RNA

20 Splicing Transcript Yields Mature mRNA

Splicing Transcript Yields Mature mRNA

21 Mature mRNA contains Coding Region and 5’ and 3’ Untranslated Regions

Mature mRNA contains Coding Region and 5’ and 3’ Untranslated Regions

22 Mature mRNA contains 7-Methyl-Guanosine 5’ Cap and 3’ Poly A Tail

Mature mRNA contains 7-Methyl-Guanosine 5’ Cap and 3’ Poly A Tail

23 ESTs, Full Length cDNA UniGene & RefSeq Databases

ESTs, Full Length cDNA UniGene & RefSeq Databases

24 ESTs, Full Length cDNA UniGene & RefSeq Databases

ESTs, Full Length cDNA UniGene & RefSeq Databases

Protein

5’ UTR

3’ UTR

5’ UTR

3’ UTR

25 GENSCAN Gene Model http://genes

GENSCAN Gene Model http://genes

mit.edu/GENSCAN.html

Hidden Markov models of gene structure

26 Genome Databases

Genome Databases

27 Entrez Gene Loci http://www

Entrez Gene Loci http://www

ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene

Entrez Gene

28 Alternative Splicing Generates Distinct Proteins in Different Tissues

Alternative Splicing Generates Distinct Proteins in Different Tissues

Gene

Transcript

mRNA-1

3’

5’

Transcript

mRNA-2

5’

3’

Exon

Exon

Intron

Intron

Exon

Splicing

Alternate Splicing

Promoter

Terminator

29 Alternative Splicing Detected in EST Libraries

Alternative Splicing Detected in EST Libraries

30 NCBI Genomes http://www

NCBI Genomes http://www

ncbi.nlm.nih.gov/sites/entrez?db=genome

31 Eukaryote Genome Projects http://www

Eukaryote Genome Projects http://www

ncbi.nlm.nih.gov/genomes/leuks.cgi

32 Canis lupus familiaris Genome http://www

Canis lupus familiaris Genome http://www

ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=Retrieve&dopt=Overview&list_uids=10726

33 NCBI Entrez Gene http://www

NCBI Entrez Gene http://www

ncbi.nlm.nih.gov/sites/entrez?db=gene

34 NCBI Entrez Gene: Human Opsin http://www

NCBI Entrez Gene: Human Opsin http://www

ncbi.nlm.nih.gov/gene?term=human%20opsin

35 Entrez Gene: Human Opsin OPN1MW http://www

Entrez Gene: Human Opsin OPN1MW http://www

ncbi.nlm.nih.gov/gene/2652

36 Entrez Gene: Human Opsin OPN1MW http://www

Entrez Gene: Human Opsin OPN1MW http://www

ncbi.nlm.nih.gov/gene/2652

37 MapViewer: Human Opsin OPN1MW http://www

MapViewer: Human Opsin OPN1MW http://www

ncbi.nlm.nih.gov/gene/2652

38 Evidence Viewer for OPN1MW http://www

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

39 OMIM Home Page http://www

OMIM Home Page http://www

ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

40 Colorblindness in OMIM

Colorblindness in OMIM

41 Colorblindness in OMIM http://omim

Colorblindness in OMIM http://omim

org/entry/303800

42 Human Genome Resources http://www

Human Genome Resources http://www

ncbi.nlm.nih.gov/genome/guide/human/

43 RefSeq http://www

RefSeq http://www

ncbi.nlm.nih.gov/RefSeq/

44 RefSeq Gene http://www

RefSeq Gene http://www

ncbi.nlm.nih.gov/refseq/rsg/

45 NCBI UniGene http://www

NCBI UniGene http://www

ncbi.nlm.nih.gov/sites/entrez?db=unigene

46 NCBI Homologene Database http://www

NCBI Homologene Database http://www

ncbi.nlm.nih.gov/homologene

47 Comparative Genomics

Comparative Genomics

48 Ensembl Home Page http://www

Ensembl Home Page http://www

ensembl.org/

49 EBI Genomes Home Page http://www

EBI Genomes Home Page http://www

ensembl.org/

50 Ensembl Human Genome http://www

Ensembl Human Genome http://www

ensembl.org/Homo_sapiens/

51 Ensembl Human Opsin Search http://uswest

Ensembl Human Opsin Search http://uswest

ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;idx=;q=opsin

52 Ensembl Human Opsin Genes http://uswest

Ensembl Human Opsin Genes http://uswest

ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;idx=;q=opsin

53 Ensembl Human OPN1MW Gene http://uswest

Ensembl Human OPN1MW Gene http://uswest

ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000147380;r=X:153448107-153461633

54 Ensembl Opsin OPN1MW Gene Location http://uswest

Ensembl Opsin OPN1MW Gene Location http://uswest

ensembl.org/Homo_sapiens/Location/View?h=Havana%20gene;r=X:153448107-153461633#r=X:153448109-153461632

55 Ensembl OPN1MW Transcripts http://uswest

Ensembl OPN1MW Transcripts http://uswest

ensembl.org/Homo_sapiens/Location/View?h=Havana%20gene;r=X:153448107-153461633#r=X:153448109-153461632

56 Ensembl OPN1MW Opsin Protein http://uswest

Ensembl OPN1MW Opsin Protein http://uswest

ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000147380;r=X:153448107-153461633;t=ENST00000369935

57 Ensembl Tutorials http://uswest

Ensembl Tutorials http://uswest

ensembl.org/info/website/tutorials/index.html

58 UCSC Genome Home Page http://genome

UCSC Genome Home Page http://genome

ucsc.edu/

59 UCSC Genome Browser http://genome

UCSC Genome Browser http://genome

ucsc.edu/cgi-bin/hgGateway

60 UCSC Genome Browser http://genome

UCSC Genome Browser http://genome

ucsc.edu/cgi-bin/hgGateway

61 UCSC Genome Browser http://genome

UCSC Genome Browser http://genome

ucsc.edu/cgi-bin/hgTracks?position=chrX:153485203-153499469&hgsid=216983641&knownGene=pack&hgFind.matches=uc004fkd.2,

62 UCSC Genome Browser http://genome

UCSC Genome Browser http://genome

ucsc.edu/cgi-bin/hgTracks?position=chrX:153485203-153499469&hgsid=216983641&knownGene=pack&hgFind.matches=uc004fkd.2,

63 UCSC Proteome Browser http://genome

UCSC Proteome Browser http://genome

ucsc.edu/cgi-bin/pbGateway

64 UCSC Proteome Browser http://genome

UCSC Proteome Browser http://genome

ucsc.edu/cgi-bin/pbGateway

65 UCSC Help File http://genome

UCSC Help File http://genome

ucsc.edu/goldenPath/help/hgTracksHelp.html

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