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Assignment 7: Multiple Sequence Alignment Using MUSCLE, MAFFT, and PRANK

This assignment focuses on creating multiple sequence alignments using MUSCLE, MAFFT, and PRANK with protein sequences provided on the website. You will analyze the alignments produced by these tools and compare them to the reference alignment from BAliBASE3, based on 3D structural superimpositions. The data file "BB12043" contains 34 protein sequences with 20-40% sequence identity. Be prepared to discuss the effects of these alignments in class. Note the due date for Assignment #6 and the 20 marks available for this task.

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Assignment 7: Multiple Sequence Alignment Using MUSCLE, MAFFT, and PRANK

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  1. MCB 5472 Assignment #7:Multiple sequence alignmentMarch 5, 2014

  2. Remember: • Assignment #6 is due before next Wednesday’s class • Worth 20 marks (not on assignment, sorry!) • In addition to today’s (short) assignment

  3. Today • Using the sequences on the website: • Create multiple sequence alignments using MUSCLE, MAFFT, and PRANK • Compare these to each other and the reference alignment also on the website

  4. BAliBASE3 • Based on 3D structural superimpositions that were manually adjusted to ensure proper alignment • The data file on the website is “BB12043”, containing 34 proteins sequences each having 20-40% sequence identity to each other • To discuss in 1 hour: what affect does this have? • NOTE: no benchmark is perfect, and one can certainly argue that there are flaws in this one!

  5. Alignment commands • MUSCLE: >muscle –in [input_file] –out [output_file] • MAFFT: >mafft--auto [input_file] > [output_file] • PRANK: >prank –d=[input_file] –o=[output_file]

  6. Sequence viewers • MEGA6 (Windows, Mac): http://www.megasoftware.net/ • Jalview (all platforms): http://www.jalview.org/Web_Installers/install.htm • Seaview (all platforms): http://doua.prabi.fr/software/seaview

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