1 / 39

Prosite and UCSC Genome Browser Exercise 4

Prosite and UCSC Genome Browser Exercise 4. What is a motif?. A sequence motif = a certain sequence that is widespread and conjectured to have biological significance Examples: KDEL – ER-lumen retention signal PKKKRKV – an NLS (nuclear localization signal). More loosely defined motifs.

zelda
Télécharger la présentation

Prosite and UCSC Genome Browser Exercise 4

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. Prosite and UCSC Genome BrowserExercise 4

  2. What is a motif? • A sequence motif = a certain sequence that is widespread and conjectured to have biological significance • Examples:KDEL – ER-lumen retention signalPKKKRKV – an NLS (nuclear localization signal)

  3. More loosely defined motifs • KDEL (usually)+ • HDEL (rarely) = • [HK]-D-E-L:H or K at the first position • This is called a pattern (in Biology), or a regular expression (in computer science)

  4. Syntax of a pattern • Example:W-x(9,11)-[FYV]-[FYW]-x(6,7)-[GSTNE]

  5. WOPLASDFGYVWPPPLAWSROPLASDFGYVWPPPLAWSWOPLASDFGYVWPPPLSQQQ    Patterns • W-x(9,11)-[FYV]-[FYW]-x(6,7)-[GSTNE] Any amino-acid, between 9-11 times F or Y or V

  6. Patterns - syntax • The standard IUPAC one-letter codes. • ‘x’ : any amino acid. • ‘[]’ : residues allowed at the position. • ‘{}’ : residues forbidden at the position. • ‘()’ : repetition of a pattern element are indicated in parenthesis. X(n) or X(n,m) to indicate the number or range of repetition. • ‘-’ : separates each pattern element. • ‘‹’ : indicated a N-terminal restriction of the pattern. • ‘›’ : indicated a C-terminal restriction of the pattern. • ‘.’ : the period ends the pattern.

  7. Profile-pattern-consensus consensus multiple alignment pattern [AC]-A-[GC]-T-[TC]-[GC] profile

  8. Prosite • A method for determining the function of uncharacterized translated protein sequences • DB of annotated protein families and functional sites as well as associated patterns and profiles to identify them

  9. Prosite • Entries are represented with patterns or profiles profile pattern [AC]-A-[GC]-T-[TC]-[GC] Profiles are used in Prosite when the motif is relatively divergent and it is difficult to represent as a pattern

  10. Scanning Prosite Query: pattern Query: sequence Result: all sequences which adhere to this pattern Result: all patterns found in sequence

  11. Searching Prosite with a sequence

  12. Prosite results for Hemoglobin subunit beta

  13. Prosite profile

  14. Prosite profile  sequence logo

  15. Sequence logo

  16. WebLogo http://weblogo.berkeley.edu/logo.cgi

  17. Searching Prosite with a sequence

  18. Patterns with a high probability of occurrence • Entries describing commonly found post-translational modifications or compositionally biased regions. • Found in the majority of known protein sequences • High probability of occurrence

  19. Searching Prosite with a pattern

  20. Searching Prosite with a pattern [TAFR]-W-Q-Y

  21. Searching Prosite with a Prosite AC

  22. UCSC Genome Browser

  23. Reset all settings of previous user UCSC Genome Browser - Gateway

  24. UCSC Genome Browser - Gateway

  25. UCSC Genome Browser - Gateway

  26. UCSC Genome Browser query results

  27. UCSC Genome Browser Annotation tracks Base position UCSC Genes UTR RefSeq mRNA (GenBank) Intron Vertebrate conservation CDS Single species compared Direction of transcription (<) SNPs EST based sequence Repeats

  28. USCS Gene

  29. UCSC Genome Browser - movement Zoom x3 + Center

  30. Sickle-cell anemia distr. Malariadistr. mRNA annotation track option

  31. BLAT • BLAT = Blast-Like Alignment Tool • BLAT is designed to find similarity of >95% on DNA, >80% for protein • Rapid search by indexing entire genome. Good for: • Finding genomic coordinates of cDNA • Determining exons/introns • Finding human (or chimp, dog, cow…) homologs of another vertebrate sequence • Find upstream regulatory regions

  32. BLAT on UCSC Genome Browser

  33. BLAT on UCSC Genome Browser

  34. BLAT Results

  35. BLAT Results Match Non-Match(mismatch/indel) Indel boundaries

  36. BLAT Results

  37. BLAT Results on the browser

  38. Getting DNA sequence of region

  39. Getting DNA sequence of region

More Related