CMPT 341 (Introduction to Biocomputing) Homework Assignment 2, Fall 2004 Due date: Oct 18, 2004 1. Given two strings T and P from the DNA alphabet, an integer k, and a score matrix for aligning each character in the alphabet to the others you are asked to
UC Davis Computer Science Technical Report CSE-2003-291
Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination
Dan Gusfield, Satish Eddhu, Charles Langley November 24, 2003
1 To
appear in Journal of Bioinformatics and Co
Multiple Alignment, Index Structures, Suffix Trees
Jens Stoye
stoye@TechFak.Uni-Bielefeld.DE
1
Introduction
String comparison is a fundamental task in bioinformatics. The comparison of two sequences (pairwise alignment), and how to compute good pairwise a
Multiple Sequence Alignment: A Brief Introduction
Anoop Sarkar for CMPT-825: Natural Language Processing
This is a brief summary of some of the issues in multiple sequence alignment (or in other words, computing the minimum edit distance between multiple
Ans 1 : Total no. of evolutionary steps = 10 (shown with the blue lines) So score = 10
Ans 2: There can be more than 1 trees with most parsimony now the ere can be 2 cases 1. One of the Most parsimonious trees is already a bifurcating tree 2. None of the
BCB/CprE/ComS 548 Fundamental Algorithms in Computational Biology Fall 2005 Homework 5 Due Thursday, December 8
1. (5 points) Consider the binary character matrix M and phylogenetic tree T shown below. Compute the parsimony score for M on T .
1 A 0 B 1 C
[Answer] The order that strings are aligned to Sc doesnt matter, because introducing spaces in any aligned pair of strings will not change the score of the final alignment. In the center-star method, the multiple alignment is constructed by successively a
BCB/CprE/ComS 548 Fundamental Algorithms in Computational Biology Fall 2005 Homework 1 Due Monday, September 13
1. (5 points) Find the best local alignments between the two sequences AGGCAT and GT GCT GC. Use the following scoring system: 10 for a match,
1. [Answer] (1) Algorithm unrestricted on k. Algorithm 1 Pattern Matching without length requirment t(i, 0) 0, for all i t(0, j) t(0, j - 1) + (" ", t[j]), for all j for i = 1 to m do for j = 1 to n do + (" ", T [i]) t(i - 1, j) t(i, j - 1) + (" ", P [j])
BCB 444/544 Fall 2005 Exam 2 Key
Friday, October 28
This closed-book, closed-notes 50-minute test consists of 7 questions. The number of points for each problem is indicated below. Read all questions carefully before starting. Write all your answers on th
BCB 444/544 Fall 2005 Exam 2 Key
Friday, October 28
This closed-book, closed-notes 50-minute test consists of 7 questions. The number of points for each problem is indicated below. Read all questions carefully before starting. Write all your answers on th
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Polymers
Long chain molecules consisting of a number of small repeating units called mer