Be488 Major Sem2 04

[, t \1 " P' .tlJj I 1'1' ( '(1"., -f ;~ ;, ! J I, , ~ I , ~. i 'I '\ ; " i , ~ 8t ) A } ftY1 ~q ~. ., . 1 t~ r , '" I~ ---1 I ~ -+:~ Department of Biochemical Engineering and HiotechnoJog)' BE488: Bioinformatics (~lajor Exam) Dated: 6.5.04 Tim : 2 hours nswer all the questions I(a) Draw the three alternati\ e unrooted trees for four taxa whose nuclcotides at a posi ti on under consideration ar e T. T. C, and C. Label ea ch of the internalnodes with the most likel~' candidates for inferred ancestral sequence~ o\\' man~' of the" possible unrooted tree for the taxa used in this quest ion. arc equa1 lv parsi moniusin that they invoke a minimum of one substitution') How many invoke a minimum of t\\'o substi tut ions'1 (b) In :1gi\"en pairwise similarity matrix, find the phylogenetic distance based tree usi ng UPG~\'1A } Sta te allthe ass umptionsmade in developingthis tre e, ~LIG-~ I i A I 100 I 88 i 61 : 6 I ! 591 i Iii ~q I ~ 9 . _ 7 IB ; : 100 i ).0 I) I) t c\ \ \ 100 \ 82~ 'I ., I', ! 0 I ! i -J 100 I 90 I I J:; 1 ; I . . M ~ I I I ! IVV! (c) Answer the fol lowing: 1. How many nuc1eotid~long would a DNA sequence need to be in order for it to not be found b)' chance more than once in a genome whose size is 3 billionbase pairs long? II. Assuming that all amino acids are utilized with the same frequency and that there are " total of approx ima tel y 1000 umqu edestina tions for a protein\vithin a eucar yotic cell,wha t is the minimumen gth that a signal sequence must be to ensure that its associated proteinw1llbe delivered appropriately? ~. , , , { J. \ t .1 r ~,; '! 1!1i (5+5+ 3 (=1. 5+1.5) marks ) 2 (a) Consider on H!\.1Mwith a sequenceofM match states each of which can genera te a letter 'x' ITom the alphabet of amino acids corresponding to a distribution P(x/mk), k = 1..,... ,\1. For each match state mk consider a delete state dk and insert state h ' LTsea dumrr.ybegin state and a dumm) end state. denoted by mo and m~I-'1espectively.dr aw the ar chitectureof such on I-L\1M mod el and label all transitionsprobab ili tiesin the diagram,Assume that transitio nsi nto mat ch or delete states alw- ays. move forward in your model, but that transi ti on into insert states do not move forward- . (b) The differenc esbetween loc a!and globalsequencealgor. thms have alreadybee n di sc us se d i1ldetails. \\"hat are s;milarities between them? (10+3 mar ks) . ..... ~""l . \ :>.

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Be488 Major Sem2 04