1. InterPro/prosite UCSC Genome Browser Exercise 3

2. 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

3. 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 Domains are structural units that carry out a certain function The same domains are The same domains are shared between different proteins Motifs are shorter Motifs are shorter sequences with certain biological activity

4. http://www.ebi.ac.uk/interpro/

5. InterPro  An integrated documentation resource for protein families, domains and sites  Groups signatures describing the same protein family or domain  Combines a number of databases that use different methodologies to derive protein signature: UniProt: UniProtKB Swiss-Prot, TrEMBL, UniRef,UniParc UniProt: UniProtKB Swiss-Prot, TrEMBL, UniRef,UniParc prosite: documented DB on domains, families and functional sites. prosite: documented DB on domains, families and functional sites. Pfam: a DB of protein families represented by MSAs Pfam: a DB of protein families represented by MSAs

6. Member databases  Sequence-motif methods: Protein signature DBs with different focus Protein signature DBs with different focus  Sequence-cluster methods: Hierarchically clustered sequence/structure DBs Hierarchically clustered sequence/structure DBs

7. InterPro search

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

11. prosite  A method for determining the function of uncharacterized translated protein sequences  Consists of a DB of annotated biologically important sites/patterns/motifs/signature/fingerprints

12. prosite  Entries are represented with patterns or profiles pattern 54321.0010.66A.1000T.00.6600.33C.00.3300G profile [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

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

14. 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

15. prosite sequence query

17. prosite pattern query

20. UCSC Genome Browser

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

24. UCSC Genome Browser query results

25. UCSC Genome Browser Annotation tracks Vertebrate conservation mRNA (GenBank) RefSeq UCSC Genes Base position Single species compared SNPs Repeats Gene Direction Exon Intron UTR

26. USCS Gene

27. UCSC Genome Browser - movement Zoom x3 + Center

28. UCSC Genome Browser – Base view

29. Annotation track options dense squish full pack

30. Annotation track options Another option to toggle between ‘pack’ and ‘dense’ view is to click on the track title Sickle-cell anemia distr. Malaria distr.

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: 1. Finding genomic coordinates of cDNA 2. Determining exons/introns 3. Finding human (or chimp, dog, cow…) homologs of another vertebrate sequence

32. BLAT on UCSC Genome Browser

34. BLAT Results

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

36. BLAT Results

37. BLAT Results on the browser

38. Getting DNA sequence of region