1 / 64

Genomics: READING genome sequences ASSEMBLY of the sequence ANNOTATION of the sequence

For Bioinformatics. , Start with:. Genomics: READING genome sequences ASSEMBLY of the sequence ANNOTATION of the sequence. carry out dideoxy sequencing. connect seqs. to make whole chromosomes. find the genes!. For Bioinformatics. , Start with:. Genomics: READING genome sequences

ciara-rojas
Télécharger la présentation

Genomics: READING genome sequences ASSEMBLY of the sequence ANNOTATION of the sequence

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. For Bioinformatics , Start with: Genomics: READING genome sequences ASSEMBLY of the sequence ANNOTATION of the sequence carry out dideoxy sequencing connect seqs. to make whole chromosomes find the genes!

  2. For Bioinformatics , Start with: Genomics: READING genome sequences ASSEMBLY of the sequence ANNOTATION of the sequence carry out dideoxy sequencing connect seqs. to make whole chromosomes find the genes!

  3. 2 ways to annotate eukaryotic genomes: -ab initio gene finders: Work on basic biological principles: Open reading frames Consensus splice sites Met start codons ….. -Genes based on previous knowledge….EVIDENCE of message 2 ways to annotate eukaryotic genomes: -ab initio gene finders: -Genes based on previous knowledge….EVIDENCE of message

  4. 2 ways to annotate eukaryotic genomes: -ab initio gene finders: Work on basic biological principles: Open reading frames Consensus splice sites Met start codons ….. -Genes based on previous knowledge….EVIDENCE of message cDNA sequence of the gene’s message cDNA of a closely related gene’ message sequence Protein sequence of the known gene Same gene’s Same gene’s from another species Related gene’s protein…….

  5. Information for Ab initio gene finding start and stop site predictions Unique identifiers Splice site predictions Homology based exon predictions computational exon predictions Tracking information Consensus gene structure (both strands)

  6. Automatically generated annotation

  7. A zebrafish hit shows a gene model protein encoded by a 6 exon gene. This gene structure (intron/exon) is seen in other species, as is the protein size. The proteins, if corresponding to MSP in S. gal., must be heavily glycosylated (likely). At least some have a signal peptide.

  8. The zebrafish hit can be viewed at higher resolution, and…

  9. The zebrafish hit can be viewed down to nucleotide resolution GO LIVE!

  10. Sarin et al

  11. Sarin et al

  12. Is there linkage between a mutant gene/phenotype and a SNP? USE standard genetic mapping technique, with SNP alternative sequences as “phenotype” B= bad hair, Dominant SNP1 ..ACGTC.. SNP1’ ..ACGCC.. SNP2 ..GCTAA.. SNP2’ ..GCAAA.. SNP3 ..GTAAC.. SNP3’ ..GTCAC.. X F1 B X START with Inbred lines- SNPs are homozygosed SNP1’ ..ACGCC.. SNP1’ ..ACGCC.. SNP2’ ..GCAAA.. SNP2’ ..GCAAA.. SNP3’ ..GTCAC.. SNP3’ ..GTCAC.. SNP1 ..ACGTC.. SNP1 ..ACGTC.. SNP2 ..GCTAA.. SNP2 ..GCTAA.. SNP3 ..GTAAC.. SNP3 ..GTAAC..

  13. Is there linkage between a mutant gene/phenotype and a SNP? USE standard genetic mapping technique, with SNP alternative sequences as “phenotype” B= bad hair, Dominant B 2’ / b 2 SNP1 ..ACGTC.. SNP1’ ..ACGCC.. SNP2 ..GCTAA.. SNP2’ ..GCAAA.. SNP3 ..GTAAC.. SNP3’ ..GTCAC.. X 1’/11/1 B/b b/b 2’/2 2/2 3’/3 3/3 2’/2 47% 2/2 3% 2’/2 3% 2/2 47% 3’/3 25% 3/3 25% 3’/3 25% 3/3 25% 1’/1 25% 1/1 25% 1’/1 25% 1/1 25% B/b B/b b/b b/b SO…B is 6 cM from SNP2, and is unlinked to SNP 1 or 3

  14. Is there linkage between a mutant gene/phenotype and a SNP? USE standard genetic mapping technique, with SNP alternative sequences as “phenotype” B= bad hair, Dominant SNP1 ..ACGTC.. SNP1’ ..ACGCC.. SNP2 ..GCTAA.. SNP2’ ..GCAAA.. SNP3 ..GTAAC.. SNP3’ ..GTCAC.. X 1/1’1/1 B/b b/b 2/2’ 2/2 3/3’ 3/3 We have the ENTIRE genome sequence of mouse, so we know where the SNPs are Now-do this while checking the sequence of THOUSANDS of SNPs SO…B is 6 cM from SNP2, and is unlinked to SNP 1 or 3

  15. Genomics: READING genome sequences ASSEMBLY of the sequence ANNOTATION of the sequence carry out dideoxy sequencing connect seqs. to make whole chromosomes find the genes! But Bioinformatics is more…

  16. End Reads (Mates) Primer SEQUENCE TRANSCRIPTOMICS: cDNAs & ESTs: Expressed Sequence Tags RNA target sample cDNA Library Each cDNA provides sequence from the two ends – two ESTs

  17. Protein sequence: from peptide sequencing, or from translation of sequenced nucleic acids !!AA_SEQUENCE 1.0 ab025413 peptide tenm4.pep Length: 2771 May 12, 1999 09:34 Type: P Check: 2254 .. 1 MDVKERKPYR SLTRRRDAER RYTSSSADSE EGKGPQKSYS SSETLKAYDQ 51 DARLAYGSRV KDMVPQEAEE FCRTGTNFTL RELGLGEMTP PHGTLYRTDI 101 GLPHCGYSMG ASSDADLEAD TVLSPEHPVR LWGRSTRSGR SSCLSSRANS 151 NLTLTDTEHE NTETDHPSSL QNHPRLRTPP PPLPHAHTPN QHHAASINSL 201 NRGNFTPRSN PSPAPTDHSL SGEPPAGSAQ EPTHAQDNWL LNSNIPLETR 251 NLGKQPFLGT LQDNLIEMDI LSASRHDGAY SDGHFLFKPG GTSPLFCTTS 301 PGYPLTSSTV YSPPPRPLPR STFSRPAFNL KKPSKYCNWK CAALSAILIS 351 ATLVILLAYF VAMHLFGLNW HLQPMEGQMQ MYEITEDTAS SWPVPTDVSL 401 YPSGGTGLET PDRKGKGAAE GKPSSLFPED SFIDSGEIDV GRRASQKIPP

  18. Structural proteomics: Coordinates, rather than 1D sequence, Saved

  19. /TRANSCRIPTOMICS (Arrays)

  20. Where? When? Who? are the RNAs RNA for ALL C. elegans genes

  21. Where? When? Who? are the RNAs

  22. Where? When? Who? are the RNAs

  23. Where? When? Who? are the RNAs MICROARRAY ANALYSIS

  24. /TRANSCRIPTOMICS (Arrays)

  25. Where? When? Who? are the RNAs Figure 4.15 Microarray Technique

  26. Where? When? Who? are the RNAs Figure 4.15 Microarray Technique

  27. Where? When? Who? are the RNAs Array analysis: see animation from Griffiths

  28. Where? When? Who? are the RNAs Figure 4.16(1) Microarray Analysis of Those Genes Whose Expression in the Early Xenopus Embryo Is Caused by the Activin-Like Protein Nodal-Related 1 (Xnr1)

  29. Where? When? Who? are the RNAs Figure 4.16(2) Microarray Analysis of Those Genes Whose Expression in the Early Xenopus Embryo Is Caused by the Activin-Like Protein Nodal-Related 1 (Xnr1)

  30. Where? When? Who? are the RNAs

  31. Where? When? Who? are the RNAs

  32. RNAi for every C. elegans gene too! -results on the web Projects to systematically Knock-out (or pseudo-knockout) every gene, in order to establish phenotype of each gene -> function of each gene

  33. Figure 4.23(1) Use of Antisense RNA to Examine the Roles of Genes in Development (here fly)

  34. Figure 4.23(2) Use of Antisense RNA to Examine the Roles of Genes in Development (here fly)

  35. RNAi for ALL C. elegans genes

  36. Figure 4.24 Injection of dsRNA for E-Cadherin into the Mouse ZygoteBlocks E-Cadherin Expression

  37. MODENCODE

  38. MODENCODE

  39. MODENCODE

  40. MODENCODE

  41. MODENCODE

  42. MODENCODE

  43. MODENCODE

  44. MODENCODE

More Related