BIOC3608 Introduction to Bioinformatics 2006

BIOC3608 Introduction to Bioinformatics 2006 - B IOC3608...

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BIOC3608 Introduction to Bioinformatics 2006 1(a). For D-Y pair, the score is -3 which is a negative score. Negative score indicates this two is just a random alignment. For D-E pair, the score is +2 which is a positive score. Positive score indicates this two is homolog. For D-S pair, the score is 0. A zero score indicates no preference. 1(b). BLOSUM matrices are constructed for different evolutionary distances. Lower BLOSUM series for alignments between distantly related proteins. Higher BLOSUM series for alignments between closely related proteins. 2(a). 1. Align each sequence with every other sequence using a pairwise alignment method. E.g. dynamic programming, approximate (fast) method: (wordsearch) 2. From the alignment scores calculate a matrix of approximate distance between each pair of sequences 3. Use this “distance matrix” to establish an approximate phylogenetic tree 4. The branch order of the tree is used to determine the order of condition of sequences to the multiple alignment 5. Align the 2 most closely related sequences and subsequently add the next closest sequence or sequence
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