MICB 405 Bioinformatics Mini-Lab #4 ClustalX Dr. Joanne

MICB 405 Bioinformatics Mini-Lab #4  ClustalX Dr. Joanne

MICB 405 Bioinformatics Mini-Lab #4 ClustalX Dr. Joanne Fox [email protected] 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.

Objectives By the end of todays 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. 2 The Globin Genes Hemoglobin is an abundant protein in red blood cells that contains two copies of globin and two copies of globin.

2002 by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter. 3 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 4 Find clustalx1.83 File

5 Right Click clustalx1.83 and Extract Here with 7-Zip Option 6

Double Click clustalx File Clustalx.exe 7 Starting up ClustalX File:

-Load sequences Edit: -Remove all gaps Alignment: -Do complete alignment -Alignment parameters

Trees: -Bootstrapped NJ -Output format options Name Window

Sequence Window 8 Load the sequences globin.pep

9 Alignment > Do Complete Alignment 10 Examine Alignment

Identity/Conservation Sequence Order Alignment Position Score skyline

11 Alignment Menu 12 Edit Menu

13 File Menu 14 Phylogenetic Tree Building

15 Trees Menu 16 Use NJPlot to visualize the trees http://pbil.univ-lyon1.fr/software/njplot.html

Google: njplot 17 Extract njplotWIN95.exe and run njplot.exe self-extract

to folder njplotWIN95.exe 18 NJPlot

19 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. 20 Links ClustalX http://bips.u-strasbg.fr/en/Documentation/ClustalX/ The web version: ClustalW

http://www.ebi.ac.uk/clustalw/ NJ-Plot http://pbil.univ-lyon1.fr/software/njplot.html Tree View (software for tree visualization) http://taxonomy.zoology.gla.ac.uk/rod/treeview.html 21

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