pattern matching 2003lec31

8/9/2019 pattern matching 2003lec31

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Pattern Matching

Rhys Price Jones

Anne R. Haake


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What is pattern matching?

Pattern matching is the procedure of

scanning a nucleic acid or protein sequence

for matches to short sequence patterns

!taden "##$%.


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Why search for patterns?

&sually the sequences of interest the query

sequences% are kno'n to (e indicators of

some important (iological function

!earch for patterns in nucleotide sequence

) *+A or R+A

!earch for patterns in amino acid sequence


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Motif

multiples uses of the 'ord

*ef, a pattern- typically is used to refer to a

short up to ten (ases or residues% repeated

or consered pattern in nucleic acids or

proteins

*ef, a short consered sequence in a protein-

usually associated 'ith function) in a (roader sense/ motif is used for all locali0ed

regions of homology/ regardless of si0e


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!ome e1amples of patterns in *+A

sequence,

Restriction sites,recognition sites for the

restriction endonucleases 2ntron splice sites

3odons specifying 4R5s

Promoters

*+A (inding sites for regulatory proteins


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Restriction !ites

Why identify them?

61act or ine1act matches?

61amples,

Restriction sites


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!plice !ites

!plice donor and splice acceptor are consensus sequences

)A statistical determination of the

pattern-appro1imates the pattern

3orA%A7879Aor7%A79 :donor: splice site

9or3%n+3or9%A787 :acceptor: splice site

!plice site e1ample


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!plice !ites

Remem(er that they are consensus sequences

Why are splice sites of interest?

) 7ene finding

) Mutations in consensus sequence at the splice ;unctionscommon in many inherited disorders

61, thalassemias/ muscular dystrophy/ 9ay

neurofi(romatosis/ *arier=s disease>>..

4ne of the thalassemias, mutation at splice acceptor

YYYNCAG| normal

YYYNCGG| mutant


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3odons !pecifying 4R5s

4R5s open reading frames%

!tart codon >.$


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Promoters

Prokaryotic promoters, 3onsensus sequences TTGACA ---- 171 ----TATAAT

-35 -10

6ukaryotic promoters) 9A9A (o1 at )@ relatie to transcriptional start site consensus is =


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9ranscription 5actor Finding !ites

Regulatory transcription factors are

sequence


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!ome e1amples of patterns in protein

sequences motifs%,

Prediction of secondary and tertiary

structure

) e.g. transcription factors

heli1


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61act s 2ne1act Appro1imate% Pattern

Matching

61act Pattern Matching

) Gimited use in (ioinformatics

) Well


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4ther uses of e1act pattern matching?

3heck P3R primers?

Annotation? te1t matching%


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Why search for patterns?

Pattern matching in sequences is also the

(asis of searching through a sequence

data(ase

) !equence alignment


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Pair'ise !equence Alignment

An alignment (et'een @ sequences is a

pair'ise match (et'een sequences.

Pair'ise sequence comparison is the primary

means of linking (iological function to the

genome and of propagating kno'n

information from one genome to another7i(as Jam(eck%

.


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Why are ine1act pattern matches releant

in sequence alignments?

!equencing errors

Mutation) @ primary types point mutations affect a single nucleotide%

segmental mutations affect a fe' to hundreds of

ad;oining nucleotides%

) su(stitutions transitions/ transersions%

) insertions/ deletions


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Mutations

Point mutations usually occur from a nucleotidemismatch that (ecomes Ifi1ed during the process ofreplication) 6scapes the *+A repair mechanism

!ignificant 'hen occur 'ithin a coding region andalso cause a change in functionality) +on


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6olutionary 3onsiderations

9hrough time mutations tend to (e presered

if they are not deleterious

5unctionally important sequences tend to (e

consered

+on


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6olutionary 3onsiderations

9he tendency of functionally important

sequences to remain relatiely unchanged

oer time is the (asis for sequence analysis

)Allo's us to dra' eolutionary connections among

genes that are related in sequence

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pattern matching 2003lec31