Prosite and Prosite and UCSC Genome UCSC Genome
BrowserBrowser
Exercise 4Exercise 4
What is a motif?What is a motif?
A sequence motifA sequence motif = a certain sequence = a certain sequence that is widespread and conjectured to that is widespread and conjectured to have biological significancehave biological significance
Examples:Examples:KDELKDEL – ER-lumen retention signal – ER-lumen retention signalPKKKRKVPKKKRKV – an NLS (nuclear localization – an NLS (nuclear localization signal)signal)
More loosely defined motifsMore loosely defined motifs
KDEL (usually)KDEL (usually)++
HDEL (rarely) HDEL (rarely) ==
[HK]-D-E-L:[HK]-D-E-L:H H oror K at the first position K at the first position
This is called a pattern (in Biology), or a This is called a pattern (in Biology), or a regular expression (in computer science)regular expression (in computer science)
Syntax of a patternSyntax of a pattern
Example:Example: W-x(9,11)-[FYV]-[FYW]-x(6,7)-[GSTNE]W-x(9,11)-[FYV]-[FYW]-x(6,7)-[GSTNE]
PatternsPatterns
W-x(9,11)-[FYV]-[FYW]-x(6,7)-[GSTNE]W-x(9,11)-[FYV]-[FYW]-x(6,7)-[GSTNE]
Any amino-acid, between 9-11
times
F or Y or
V
WOPLASDFGYVWPPPLAWSROPLASDFGYVWPPPLAWSWOPLASDFGYVWPPPLSQQQ
Patterns - syntaxPatterns - syntax
The standard IUPAC one-letter codes. The standard IUPAC one-letter codes. ‘‘x’x’ : any amino acid. : any amino acid. ‘‘[]’[]’ : residues allowed at the position. : residues allowed at the position. ‘‘{}’{}’ : residues forbidden at the position. : residues forbidden at the position. ‘‘()’()’ : repetition of a pattern element are indicated in : repetition of a pattern element are indicated in
parenthesis. X(n) or X(n,m) to indicate the number or parenthesis. X(n) or X(n,m) to indicate the number or range of repetition. range of repetition.
‘‘-’-’ : separates each pattern element. : separates each pattern element. ‘‹’‘‹’ : indicated a N-terminal restriction of the pattern. : indicated a N-terminal restriction of the pattern. ‘›’‘›’ : indicated a C-terminal restriction of the pattern. : indicated a C-terminal restriction of the pattern. ‘‘.’.’ : the period ends the pattern. : the period ends the pattern.
Profile-pattern-consensusProfile-pattern-consensus
AAAACCTTTTGG
AAAAGGTTCCGG
CCAACCTTTTCC
1122334455
AA0.660.66110000..
TT00000011..
CC0.330.33000.660.6600..
GG00000.330.3300..
AAAACCTTTTGG
]AC-[A-[GC]-T-[TC]-[GC]
multiple alignment
consensus
pattern
profile
NNAANNTTNNNN
PrositeProsite
A method for determining the function of A method for determining the function of uncharacterized translated protein uncharacterized translated protein sequencessequences
DB of annotated protein families and DB of annotated protein families and functional sites as well as associated functional sites as well as associated patterns and profiles to identify thempatterns and profiles to identify them
PrositeProsite Entries are represented with Entries are represented with patternspatterns or or
profilesprofiles
pattern
1122334455
AA0.660.66110000..
TT00000011..
CC0.330.33000.660.6600..
GG00000.330.3300..
profile
]AC-[A-[GC]-T-[TC]-[GC]
Profiles are used in Prosite when the motif is relatively Profiles are used in Prosite when the motif is relatively divergent and it is difficult to represent as a patterndivergent and it is difficult to represent as a pattern
Scanning PrositeScanning Prosite
Query: sequence
Query: pattern
Result: all patterns found in sequence
Result: all sequences which adhere to this pattern
Searching Prosite with a sequenceSearching Prosite with a sequence
PrositeProsite results for Hemoglobin subunit beta results for Hemoglobin subunit beta
Prosite profileProsite profile
Prosite profile Prosite profile sequence logo sequence logo
Sequence logoSequence logo
WebLogoWebLogo
http://weblogo.berkeley.edu/logo.cgi
Searching Prosite with a sequenceSearching Prosite with a sequence
Patterns with a high probability of Patterns with a high probability of occurrenceoccurrence
Entries describing commonly found postEntries describing commonly found post--translational modifications or compositionally translational modifications or compositionally biased regions.biased regions.
Found in the majority of known protein Found in the majority of known protein sequences sequences
High probability of occurrenceHigh probability of occurrence
Searching Prosite with a patternSearching Prosite with a pattern
Searching Prosite with a patternSearching Prosite with a pattern
]TAFR-[W-Q-Y
Searching Prosite with a Prosite ACSearching Prosite with a Prosite AC
UCSC Genome BrowserUCSC Genome Browser
Reset all settings of
previous user
UCSC Genome Browser - GatewayUCSC Genome Browser - Gateway
UCSC Genome Browser - GatewayUCSC Genome Browser - Gateway
UCSC Genome Browser - GatewayUCSC Genome Browser - Gateway
UCSC Genome Browser query resultsUCSC Genome Browser query results
UCSC Genome Browser UCSC Genome Browser Annotation tracksAnnotation tracks
Vertebrate conservation
mRNA (GenBank)
RefSeq
UCSC Genes
Base position
Single species compared
SNPs
Repeats
Direction of transcription (<)
CDS
Intron
UTR
EST based sequence
USCS GeneUSCS Gene
UCSC Genome Browser - movementUCSC Genome Browser - movement
Zoom x3 + Center
mRNA mRNA annotation track optionannotation track option
Sickle-cell anemia distr.
Malariadistr.
BLATBLAT
BLAT = BBLAT = Blast-last-LLike ike AAlignment lignment TTool ool BLAT is designed to find similarity of BLAT is designed to find similarity of >95% on >95% on
DNADNA, , >80% for protein>80% for protein Rapid search by indexing entire genome.Rapid search by indexing entire genome.Good for:Good for:1.1. Finding genomic coordinates of cDNAFinding genomic coordinates of cDNA2.2. Determining exons/intronsDetermining exons/introns3.3. Finding human (or chimp, dog, cow…) Finding human (or chimp, dog, cow…)
homologs of another vertebrate sequencehomologs of another vertebrate sequence4.4. Find upstream regulatory regionsFind upstream regulatory regions
BLAT on UCSC Genome BrowserBLAT on UCSC Genome Browser
BLAT on UCSC Genome BrowserBLAT on UCSC Genome Browser
BLAT ResultsBLAT Results
BLAT ResultsBLAT Results
Match
Non-Match(mismatch/indel)
Indel boundaries
BLAT ResultsBLAT Results
BLAT Results on the browserBLAT Results on the browser
Getting Getting DNADNA sequence of region sequence of region
Getting Getting DNADNA sequence of region sequence of region