InterPro/prosite UCSC Genome Browser Exercise 3

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InterPro/prosite UCSC Genome
BrowserExercise 3
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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

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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

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http//www.ebi.ac.uk/interpro/
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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
• prosite documented DB on domains, families and
  functional sites.
• Pfam a DB of protein families represented by MSAs

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Member databases

• Sequence-motif methods
• Protein signature DBs with different focus

• Sequence-cluster methods
• Hierarchically clustered sequence/structure DBs

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InterPro search
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http//www.expasy.ch/prosite/
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prosite

• A method for determining the function of
  uncharacterized translated protein sequences
• Consists of a DB of annotated biologically
  important sites/patterns/motifs/signature/fingerpr
  ints

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prosite

• Entries are represented with patterns or profiles

profile
5 4 3 2 1
. 0 0 1 0.66 A
. 1 0 0 0 T
. 0 0.66 0 0.33 C
. 0 0.33 0 0 G
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

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

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prosite sequence query
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prosite pattern query
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UCSC Genome Browser
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UCSC Genome Browser - Gateway
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UCSC Genome Browser - Gateway
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UCSC Genome Browser - Gateway
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UCSC Genome Browserquery results
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UCSC Genome Browser Annotation tracks
Base position
UCSC Genes
UTR
RefSeq
mRNA (GenBank)
Intron
Exon
GeneDirection
SNPs
Repeats
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USCS Gene
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UCSC Genome Browser - movement
Zoom x3 Center
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UCSC Genome Browser Base view
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Annotation track options
dense
squish
pack
full
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Annotation track options
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BLAT

• BLAT Blast-Like Alignment Tool
• BLAT is designed to find similarity of gt95 on
  DNA, gt80 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

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BLAT on UCSC Genome Browser
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BLAT on UCSC Genome Browser
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BLAT Results
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BLAT Results
Match
Non-Match(mismatch/indel)
Indel boundaries
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BLAT Results
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BLAT Results on the browser
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Getting DNA sequence of region
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Getting DNA sequence of region