ELE 4120 Bioinformatics Tutorial 1

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Description

ELE 4120 BioinformaticsTutorial 3Content• Dot (Matrix) Plots• Simple Alignments•Gaps– Simple gap penalties– Orientation and length penaltiesDot Plots (1)• Evaluating similarity between 2 sequences• Window size – number of nucleotides compare each time (usually odd number)• Stringency – the minimum number of nucleotides in the window must be “match”, so that a dot can be placed• Mismatch Limit – the maximum number of nucleotides in the window can be “not match”, so that a dot can still be placed • Mismatch Limit = Window size - StringencyDot Plots (2)• Example 1: Compare the following sequences, with window size = 5, stringency = 3AGAGACTCAGAGTGTGA G A G A C T C A G A G A C T C A G A G A C T CA A AG G GA ● A A ●G G GT T TG GGT TTG GG0 match 4 matches4 matchesDot Plots (3)A G A G A C T CA G A G A C T C A G A G A C T CA A AGG GA A AG ●G GT T TGG GT T TGG G0 match 0 match 3 matchesA G A G A C T CAGA ● ●Final answerG ● ●T ●GTGDot Plots (4)• Example 2: Compare the following sequences and find the regions of similarity between two sequences. (window size = 5, stringency = 3)TGACCATGGGGTACCAGC• Dot plots:region of similarityT G A C C A T G GGGTA ●region of similarityC ●C ●A ●GCSimple Alignments• Homologs – sequences that share a common ancestor• 3 possible changes occur at sequence– MutationChange the – Add one or more positions sequence length– Delete one or more positionsSimple ...

Informations

• Publié par: Thoim
• Nombre de lectures: 31
• Langue: English

Extrait

ELE 4120 Bioinformatics

Tutorial 3

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Content

Dot (Matrix) Plots

Simple Alignments

Gaps

 Simple gap penalties

 Orientation and length penalties

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Dot Plots (1)

Evaluating similarity between 2 sequences

Window size  number of nucleotides compare each time (usually odd number)

Stringency  the minimum number of nucleotides in the window must be match, so that a dot can be placed

Mismatch Limit  the maximum number of nucleotides in the window can be  not match, so that a dot can still be placed

Mismatch Limit = Window size - Stringency

Dot Plots (2)

 Example 1: Compare the following sequences, with window size = 5, stringency = 3

A G A G T G T G

A G A G A C T C

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4 matches

AGAGACTC AGAGTGTG

A G A G A C T C A G A G T G T G

0 match

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A G A G A C T C A G A G T G T G

4 matches

A G A G A C T C A G A G T G T G

0 match

Final answer

Dot Plots (3) A G A G A C T C  A G A G A C T C A A G G A A G G T T G G T T G G

A G A G T G T G

0 match

A G A G A C T C

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3 matches

Dot Plots (4)  Example 2: Compare the following sequences and find the regions of similarity between two sequences. (window size =   5, stringency = 3)  TGACCATGG

 Dot plots:

region of similarity

G G T A C C A G C

GGTACCAGC

region of similarity

T G A C C A T G G

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Simple Alignments

Homologs  sequences that share a common ancestor

3 possible changes occur at sequence

 Mutation

 Add one or more positions  Delete one or more positions

Change the 

sequence length

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Simple Alignments  No gap(1)

For 2 sequences with different lengths and no gap is inserted Obtain the optimal alignment by sliding the shorter sequence and scoring each alignment Scoring function  e.g match score =1, mismatch score= 0 Example:  Two sequences with different lengths

CGTTAGA

CGTAC

 How many possible alignments? What is the optimal alignment? If match score =1 mismatch score =0 ,

Simple Alignments No gap(2)

 Answer:  There are 3 different alignments

CGTTAGA

CGTAC

Score = 3

Optimal alignment

CGTTAGA

CGTAC

Score = 2

CGTTAGA

CGTAC

Score = 0

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Gaps

Add gaps to make lengths of 2 sequences equal

More possible alignments than simple alignment

Gap Penalty is added to the scoring function, i.e. gap penalty, match score, mismatch score

Gap penalty usually has lower score than match and mismatch score

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Simple Gap Penalty

Example

A T G C C A T

A T -- T C -- -- Calculate the score of the above alignment with gaps  if gap penalty = -1;  match score = 1;  Mismatch score = 0; Answer:  Number of match = 3 Î 3 scores  Number of mismatch = 1 Î 0 score  Number of gap = 3 Î -3 scores  Score of alignment = 3+0-3 = 0