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Sequence Analysis of Single Polymorphism in the Factor V Gene - page 13 / 15

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Biol  420                                                                                                                                          Fall 2007

xi.

Click the Browse button to set the AlignIR project directory.

xii.

Select the MyAlignIRProj directory in the file selection window and click OK.

xiii.

Click OK in the Destination window to close it.

xiv.

Since the samples are already sequenced, deselect the Run Actions After Sequencing check box.

xv.

Click Save to save changes to the action set.

xvi.

Then, click Run Now.

   4.  To perform an alignment:

b.

Open the AlignIR program and then Create a new project.

c.

To create a new project:

i.

Choose New from the File menu.  The Create New Project window is used to name new projects and their associated directories.    The Create Project Directory check box should be selected so that new directories are created for each project.  

ii.

Name the Project MCB Align and then select the Next button in the New Project window.  This will allow you to add new sample files to the Project.  Also, new sample files can be added at any time by choosing Add/Remove Samples from the File menu.

iii.

To move a file into the project, scoll through the directory tree in the lower right hand side of the window.  Open the e-Seqv3 folder, then the Data folder and then the MCB_Buccal_Trial1 folder.  Within this folder you will highlight all of the ____700 sample files (use the control key to select multiple files) and then click Add to add samples to the Align Window.  

iv.

Then click the Finish button in the Add/Remove Samples window to add the selected files to the project.  At this point the sequence should appear in the AlignIR window.

d.

Choose Align from the File menu.  Alignment will begin immediately and a progress bar shows the status of the alignment.

e.

When the alignment is finished, click OK in the Progress window to dismiss it.  The alignment is performed using a set of parameters that tell AlignIR how much to value certain characteristics of the sequence data.  The default alignment parameters provide good performance for most sequence files and rarely need changing.  However, they can be accessed and modified by choosing Alignment from the Settings menu.

  5.  Print the Alignment.  

  6.   Print Report:

a.  Go to Reports tab and select All Samples.

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