InterPro/prosite UCSC Genome Browser Exercise 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
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
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
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
InterPro search
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
prosite Entries are represented with patterns or profiles pattern A.1000T C G 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
Scanning prosite Query: sequence Query: pattern Result: all patterns found in sequence Result: all sequences which adhere to this pattern
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
prosite sequence query
prosite pattern query
UCSC Genome Browser
Reset all settings of previous user UCSC Genome Browser - Gateway
UCSC Genome Browser query results
UCSC Genome Browser Annotation tracks Vertebrate conservation mRNA (GenBank) RefSeq UCSC Genes Base position Single species compared SNPs Repeats Gene Direction Exon Intron UTR
USCS Gene
UCSC Genome Browser - movement Zoom x3 + Center
UCSC Genome Browser – Base view
Annotation track options dense squish full pack
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.
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
BLAT on UCSC Genome Browser
BLAT Results
Match Non-Match (mismatch/indel) Indel boundaries
BLAT Results
BLAT Results on the browser
Getting DNA sequence of region