Bioinformatics Online Home
   Chapters Links Problems Enroll for Updates Help
 Problem 1
 Problem 2
 Problem 3
 Problem 4
 Problem 5
 Problem 6
 Problem 7
 Problem 8
 All problems

Home  >  Problems  >  Chapter 5

1. Practice using the CLUSTALW program to align the set of proteins in the RAD51-RECA group. These proteins all promote homologous DNA strand interactions during genetic recombination between DNA molecules. The sequences may be retrieved from the SwissProt server (perform Web search to find link to SwissProt) by their accession numbers in FASTA format: P25454, P25453, P03017, P48295. Use a simple text editor to make a FASTA multiple sequence by catenating these individual sequence files into one FASTA msa file (see p. 53).
  1. Locate a CLUSTALW Web site. This program is available for PCs and also on a Web site at Baylor College of Medicine (BCM) searchlauncher site.
  2. Copy and paste the catenated FASTA sequence file into the CLUSTALW data window.
  3. Use the default alignment conditions provided by the program.
  4. Note the two kinds of msa output formats. One is the align format with numbers, and the second is the FASTA format with the aligned sequences joined end to end in FASTA format, with gaps in each sequence corresponding to the alignment.
  5. Save this file for later reference.


© 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