BSCI 348s Comparative Bioinformatics
Homework 2001
Assignment 1 (20 points, due 9/17/01)
Manually apply the Needleman-Wunsch Algorithm to determine the best alignment for the following amino acid sequences. Use a BLOSUM62 matrix for your match scores, and a gap penalty of 8. Be sure that your matrix shows the score for each cell and the traceback, and be sure that you show the alignment as well as the matrix you used to calculate it.
Sequence #1: TVVTGRVE
Sequence #2: TVATRIE
Assignment #2 (20 points, due Monday November 5)
Consider the following sequence (which is also available on UMBI in GCG format at /users/bsci348s/hwk2001-2.seq and in fasta format):
This is a (slightly modified) sequence fragment from a genome sequencing project. Your assignment is to learn as much as possible about the sequence and to report both the properties of the sequence and the analyses and evidence you used in your analysis. Your work will be graded on the completeness and accuracy with which you determine the features of the sequence, on the clarity of your presentation, and on techniques that you used in analysis. You should also speculate on the likely source of the sequence (i.e., what organism is it likely to have come from?). Your report should consist of a map of the sequence with features labeled, a brief statement (roughly one page) describing the features and how you detected them, and supplementary material that documents your work.
Assignment #3 (10 points, due Monday November 12)
Construct a fully resolved, dichotomously branching phylogeny for at least seven of the balls we had in class. You may use the tree you developed in class, or make another. Identify what characters you were using to infer this phylogeny, and code these characters into a character matrix.
Assignment #2 (50 points, due Friday December 7)
1) Prepare a codon-usage table for Plasmodium falciparum (based on at least ten genes, preferably from Chromosome 2). To do this, you should use the GCG utility codonfrequency. Present the codon usage table, along wtih the accession number and range of sequence used for each gene you use to calculate the codon usage table.
You will want to have these codon usage data available as you work on the following:
2) Consider the following sequence (which is also available on UMBI in GCG format at /users/bsci348s/hwk2001-4.seq)
This is a sequence fragment from the Plasmodium falciparum genome sequencing project. You should learn as much as possible about the sequence and to report both the properties of the sequence and the analyses and evidence you used in your analysis. Your report should consist of a linear map of the sequence with features labeled, a brief statement (roughly one page) describing the features shown on the map and how you detected them, and supplementary material that documents your work.
Your analyses should make use of GCG, but you may also take advantage of other resources we have discussed in class. Your work will be graded on the completeness and accuracy with which you determine the features of the sequence, on the clarity of your presentation, and on techniques that you used in analysis.
