Assignment 3_ans

Assignment 3_ans - Introduction to Bioinformatics/Elements...

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Introduction to Bioinformatics/Elements of Bioinformatics Assignment 3 - Answers 1a Write the following phylogenetic tree in the Newick tree format. (3%) Answer: One of several possible representations: (((A:1,B:3):3,H:4):5,(C:6,D:7):8,(G:5,(E:2,F:1):4):3); 1b. Find the root of the above tree by the mid-point rooting technique. Write the resulting rooted tree in the Newick tree format. (2%) Answer: Root is placed at the mid-point between taxa B and D. C D A B H E F G 6 7 1 3 4 2 1 5 6 3 5 4 3 2 Newick format: ((C:6,D:7):6,(((A:1,B:3):3,H:4):5,((E:2,F:1):4,G:5):3):2);
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Consider the following alignment: Seq1. CTAA G GCTTACGA TT ACGAGGATCC A AATGGCACCA A TGCT Seq2. CTA- C GCTTACGA CA ACGAGGATCC G AATGGCACCA T TGCT Calculate the Juke-Cantor distance between the 2 sequences. (2%) Answer: 0.1367 Count the number of sites that differ between seq1 and seq2, ignoring gaps: 5 Total number of sites, ignoring gaps: 40 Calculate the observed distance = 5 /40 = 0.125 Apply distance correction: 137 . 0 ) 125 . 0 3
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This note was uploaded on 07/29/2010 for the course BIOC BIOC1805 taught by Professor Dr.brianwong during the Summer '09 term at HKU.

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Assignment 3_ans - Introduction to Bioinformatics/Elements...

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