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Prosite and UCSC Genome Browser Exercise 3

Prosite and UCSC Genome Browser Exercise 3. Protein motifs and Prosite . Turning information into knowledge. The outcome of a sequencing project is masses of raw data The challenge is to turn this raw data into biological knowledge

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Prosite and UCSC Genome Browser Exercise 3

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  1. Prosite and UCSC Genome BrowserExercise 3

  2. Protein motifs andProsite

  3. Turning information into knowledge • The outcome of a sequencing project is masses of raw data • The challenge is to turn this raw data into biological knowledge • A valuable tool for this challenge is an automated diagnostic pipe through which newly determined sequences can be streamlined

  4. From sequence to function • Nature tends to innovate rather than invent • Proteins are composed of functional elements: domains and motifs • Domains are structural units that carry out a certain function • The same domains are shared between different proteins • Motifs are shorter sequences with certain biological activity

  5. 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)

  6. 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)

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

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

  9. 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.

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

  11. http://www.expasy.ch/prosite/

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

  13. 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

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

  15. prosite sequence query

  16. Prosite profile

  17. Prosite profile  sequence logo

  18. Sequence logo

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

  20. Searching Prosite with a sequence

  21. 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

  22. Searching Prosite with a pattern

  23. prosite pattern query

  24. Searching Prosite with a Prosite AC

  25. UCSC Genome Browser

  26. UCSC Genome Browser

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

  28. UCSC Genome Browser - Gateway

  29. UCSC Genome Browser - Gateway

  30. UCSC Genome Browser query results

  31. Vertebrate conservation Single species compared UCSC Genome Browser Annotation tracks Base position UCSC Genes UTR RefSeq mRNA (GenBank) Intron CDS Direction oftranscription (<) SNPs Repeats

  32. USCS Gene

  33. UCSC Genome Browser - movement Zoom x3 + Center

  34. UCSC Genome Browser – Base view

  35. Annotation track options dense squish pack full

  36. Another option totoggle between‘pack’ and ‘dense’view is to click onthe track title Sickle-cell anemia distr. Malariadistr. Annotation track options

  37. 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

  38. BLAT on UCSC Genome Browser

  39. BLAT on UCSC Genome Browser

  40. BLAT Results

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

  42. BLAT Results

  43. BLAT Results on the browser

  44. Getting DNA sequence of region

  45. Getting DNA sequence of region

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