Prosite and ucsc genome browser exercise 3
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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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Prosite and ucsc genome browser exercise 3

Prosite and UCSC Genome BrowserExercise 3


Protein motifs and prosite

Protein motifs andProsite


Turning information into knowledge

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

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


What is a motif

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)


More loosely defined motifs

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)


Syntax of a pattern

Syntax of a pattern

  • Example:W-x(9,11)-[FYV]-[FYW]-x(6,7)-[GSTNE]


Patterns

WOPLASDFGYVWPPPLAWSROPLASDFGYVWPPPLAWSWOPLASDFGYVWPPPLSQQQ

Patterns

  • W-x(9,11)-[FYV]-[FYW]-x(6,7)-[GSTNE]

Any amino-acid, between 9-11 times

F or Y or V


Patterns syntax

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.


Profile pattern consensus

Profile-pattern-consensus

consensus

multiple alignment

pattern

[AC]-A-[GC]-T-[TC]-[GC]

profile


Http www expasy ch prosite

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


Prosite

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


Prosite1

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


Scanning prosite

Scanning Prosite

Query: pattern

Query: sequence

Result: all sequences which adhere to this pattern

Result: all patterns found in sequence


Prosite sequence query

prosite sequence query


Prosite profile

Prosite profile


Prosite profile sequence logo

Prosite profile  sequence logo


Sequence logo

Sequence logo


Weblogo

WebLogo

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


Searching prosite with a sequence

Searching Prosite with a sequence


Patterns with a high probability of occurrence

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


Searching prosite with a pattern

Searching Prosite with a pattern


Prosite pattern query

prosite pattern query


Searching prosite with a prosite ac

Searching Prosite with a Prosite AC


Ucsc genome browser

UCSC Genome Browser


Ucsc genome browser1

UCSC Genome Browser


Ucsc genome browser gateway

Reset all settings of previous user

UCSC Genome Browser - Gateway


Ucsc genome browser gateway1

UCSC Genome Browser - Gateway


Ucsc genome browser gateway2

UCSC Genome Browser - Gateway


Ucsc genome browser query results

UCSC Genome Browser query results


Prosite and ucsc genome browser exercise 3

Vertebrate conservation

Single species compared

UCSC Genome Browser Annotation tracks

Base position

UCSC Genes

UTR

RefSeq

mRNA (GenBank)

Intron

CDS

Direction oftranscription (<)

SNPs

Repeats


Uscs gene

USCS Gene


Prosite and ucsc genome browser exercise 3

UCSC Genome Browser - movement

Zoom x3 + Center


Prosite and ucsc genome browser exercise 3

UCSC Genome Browser – Base view


Prosite and ucsc genome browser exercise 3

Annotation track options

dense

squish

pack

full


Prosite and ucsc genome browser exercise 3

Another option totoggle between‘pack’ and ‘dense’view is to click onthe track title

Sickle-cell anemia distr.

Malariadistr.

Annotation track options


Prosite and ucsc genome browser exercise 3

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


Blat on ucsc genome browser

BLAT on UCSC Genome Browser


Blat on ucsc genome browser1

BLAT on UCSC Genome Browser


Blat results

BLAT Results


Blat results1

BLAT Results

Match

Non-Match(mismatch/indel)

Indel boundaries


Blat results2

BLAT Results


Blat results on the browser

BLAT Results on the browser


Getting dna sequence of region

Getting DNA sequence of region


Getting dna sequence of region1

Getting DNA sequence of region


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