Open Book and Notes Midterm on Bioinformatics | ECS 124, Exams of Computer Science

Download Open Book and Notes Midterm on Bioinformatics | ECS 124 and more Exams Computer Science in PDF only on Docsity! CS 124 Winter 2008 Midterm. Open book and notes, but only course materials used in this class. 1. (20pts) Write out the dynamic programming alignment table for the optimal global alignment of the strings “global” and “local”. Put “global” on the left and “local” on the top. The objective function is to maximize the #matches - #mismatches - #spaces. Be sure to put in backpointers to allow a traceback, and show one traceback path that corresponds to an optimal alignment. Write out that alignment explicitly. Write your answer on the back of the next page. Answer: Ideally you should have written out all of the traceback arrows. Since I found there to be room for confusion I only marked off if the trace- back was not given for the optimal solution, or if attempted tracebacks were incorrect. Point allocation · match: 1 · mismatch: -1 · spaces: -1 Alignment _ L O C A L G L O B A L – – L O C A L – 0 ← -1 ← -2 ← -3 ← -4 ← -5 G ↑ -1 ↖ -1 ↖← -2 ↖ ← -3 ↖ ← -4 ↖ ← -5 L ↑ -2 ↖← 0 ← -1 ← -2 ← -3 ↖ -3 O ↑ -3 ↑ -1 ↖↑ 1 ← 0 ← -1 ← -2 B ↑ -4 ↑ -2 ↑ 0 ↖ 0 ↖↑ -1 ↖↑ -2 A ↑ -5 ↑ -3 ↑ -1 ↖↑ -1 ↖ 1 ← 0 L ↑ -6 ↖↑ -4 ↑ -2 ↖↑ -2 ↑ 0 ↖ 2 2. (10pt) When you see an alignment between two strings that is sup- posed to exhibit the biological relationship between those two strings, what does a mismatch represent biologically; what does a space represent; what 1 does a gap represent? Why was the concept of gap introduced into the align- ment model? Put this into your own words - don’t copy from the notes. Answer: A mismatch represents a point mutation of a single residue (nu- cleotide or amino acid); A space represents a indel, i.e., an event that either inserted or deleted a single residue from one of the two strings being aligned. A gap is a contiguous run of spaces, which represents any of several possible biological events that insert or delete a run of residues as a single event. In- sertion of retrotransposons is one such example. The concept of a gap was introduced into the alignment model because in many biological contexts the spaces are organized into a few gaps, rather than spread out through- out the alignment, and without an explicit term for gaps in the alignment objective function, there is no way to encourage such alignments instead of alignments where the spaces (an equal number say) are dispersed throughout the alignment. The Fitch computation early in the history of alignment was one demonstration of this. In the exam, several students talked correctly about how gaps occur in biological sequences, but did not then translate that into why in the align- ment model (and the corresponding objective function) we need an explicit term for gaps, rather than just a term for spaces. 3. (10pt) In general terms, when comparing two molecular sequences, when would you choose to use the Smith-Waterman algorithm over the Needleman-Wunsch algorithm? Or in other words, when should you use global and when local alignment? Which algorithm does local and which global? Answer: NW - global SW - local Use global when the two strings are expected to have a biological re- lationship throughout their entire lengths, reflecting a reasonable level of similarity. An example is where the strings come from a single family of pro- teins (globins say) but in different species. Use Local to identify substrings of high similarity embedded in longer strings that are not related or reasonably similar outside of the substrings of high similarity. Many biological examples of this case. 4. Recall that a substring in a string S must consist of characters that are contiguous in S. For example, for S = abcdefg, cde is a substring, while bde is not. 2