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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 ...

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