MICB 405 BioinformaticsMini-Lab #4 – ClustalX

Dr. Joanne Fox

joanne@msl.ubc.ca

We gratefully acknowledge the funding for the development of these teaching materials provided by UBC students through the Teaching and Learning Enhancement Fund (TLEF) from 2005-2007.

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Objectives

• By the end of today’s tutorial:– You will download and install ClustalX on your

own computer.– You will use ClustalX to generate a multiple

sequence alignment for a set of globin sequences.

– You will view a phylogenetic tree generated from this set of globin sequences.

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The Globin Genes

© 2002 by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter.

Hemoglobin is an abundant protein in red blood cells that contains two copies of α globin and two copies of β globin.

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Download ClustalX v1.83

• Go to: ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/

• Scroll down list and choose:– clustalx1.83.zip

• Download

• Extract all files to a fold where you can find it. ie. Desktop

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Find ‘clustalx1.83’ File

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Right Click ‘clustalx1.83’ and ‘Extract Here’ with 7-Zip Option

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Double Click ‘clustalx’ FileClustalx.exe

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Starting up ClustalX

NameWindow

SequenceWindow

File:-Load sequences

Edit:-Remove all gaps

Alignment:-Do complete alignment-Alignment parameters

Trees:-Bootstrapped NJ-Output format options

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• Load the sequences– globin.pep

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Alignment > Do Complete Alignment

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Examine Alignment

Alignment Position

Score ‘skyline’

SequenceOrder

Identity/Conservation

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Alignment Menu

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Edit Menu

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File Menu

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Phylogenetic Tree Building

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Trees Menu

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Use NJPlot to visualize the treeshttp://pbil.univ-lyon1.fr/software/njplot.html

Google: ‘njplot’

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Extract njplotWIN95.exe and run njplot.exe

njplotWIN95.exe

self-extract to folder

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NJPlot

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Trees > Bootstrap N-J Tree

1. Open tree file (.ph)2. Open bootstrap file (.phb)3. Can now display tree with both distances and/or bootstrap values.4. Can save tree as .pdf for later use in poster.

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Links

• ClustalXhttp://bips.u-strasbg.fr/en/Documentation/ClustalX/

• The web version: ClustalW http://www.ebi.ac.uk/clustalw/

• NJ-Plothttp://pbil.univ-lyon1.fr/software/njplot.html

• Tree View (software for tree visualization)http://taxonomy.zoology.gla.ac.uk/rod/treeview.html