Prosite and UCSC Genome Browser Exercise 4

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