Bioinformatics Online Home
   Chapters Links Problems Enroll for Updates Help
 Problem 1
 Problem 2
 Problem 3
 Problem 4
 Problem 5
 All problems

Home  >  Problems  >  Chapter 3


For this question, use the program LALIGN on the University of Virginia FASTA server This program aligns sequences by a local dynamic programming algorithm and includes end gap penalties. It produces as many different alignments as specified, with no two alignments including a match of the same two sequence positions.

  1. Obtain the following two sequences from GenBank in FASTA format: (P03017) from the bacterium E. coli and (P25454) from budding yeast (Saccharomyces cerevisiae). These proteins have the same function, i.e., promoting the pairing of homologous single-stranded DNAs. They almost certainly have the same three-dimensional structure but have diverged enough that they are difficult to align.
  2. Use LALIGN to align the above two sequences with gap penalties of 12 and 2. Note the length of the alignment, the percent identity, and the score of the alignment.
  3. Repeat the alignment with gap penalties of 5 and 1 and note the features of the alignment.
  4. Describe what happened when the gap penalties were reduced. Which of these alignments looks like a local alignment and which looks like a global alignment?


© 2004 by Cold Spring Harbor Laboratory Press. All rights reserved.
No part of these pages, either text or image, may be used for any purpose other than personal use. Therefore, reproduction, modification, storage in a retrieval system, or retransmission, in any form or by any means, electronic, mechanical, or otherwise, for reasons other than personal use, is strictly prohibited without prior written permission.


Home Chapters Links Problems Enroll for Updates Help CSHL Press