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MCB 5472 Assignment #7: Multiple sequence alignment March 5, 2014

MCB 5472 Assignment #7: Multiple sequence alignment March 5, 2014. Remember:. Assignment #6 is due before next Wednesday’s class Worth 20 marks (not on assignment, sorry!) In addition to today’s (short) assignment. Today. Using the sequences on the website:

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MCB 5472 Assignment #7: Multiple sequence alignment March 5, 2014

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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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