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ClustalW FAQ (Frequently Asked Questions)
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How are the pairwise
alignment scores generated?
A pairwise score is calculated for every pair of
sequences that are to be aligned. These scores are presented in a table in the
results. Pairwise scores are calculated as the number of identities in the best
alignment divided by the number of residues compared (gap positions are
excluded). Both of these scores are initially calculated as percent identity
scores and are converted to distances by dividing by 100 and subtracting from
1.0 to give number of differences per site. We do not correct for multiple
substitutions in these initial distances.
As the pairwise score is calculated independently of the
matrix and gaps chosen, it will always be the same value for a particular pair
of sequences.
Alignment score is calculated in two ways - fast and slow (more accurate mode). The scores are calculated from separate pairwise alignments. These can be calculated using 2 methods: dynamic programming (slow but accurate) or by the method of Wilbur and Lipman (extremely fast but approximate).
See also:
How can I get the colour version of the alignment?
The alignment will appear on the results page in black
and white. There is an option available 'show colours' that will display the
alignment in colour according to the physiochemical characteristics of the
amino acids.
Why
can I not see the guide tree in my browser?
You must have java enabled to see the guide tree. The
guide trees are produced by a java applet (provided by Java runtime plugin). To check that you
have enabled Java applets go to Preferences, Advanced, and "Enable
Java".
More Information
What is Jalview?
Jalview
is a mulitple alignment editor that is written entirely in java. It is provided
as an option when you retrieve a multiple alignment from ClustalW. To use it,
just click on the Jalview gif. It allows you to do things like:
- Use
many different colour schemes
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Read
and write alignments in a variety of formats
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Order
the alignment according to different criteria
-
Draw
UPGMA and NJ trees depending on percent identity criteria
-
Remove
gapped columns
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Perform
Smith-Waterman alignment of selected sequences
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Insert/delete
gaps using the mouse
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Cluster
sequences using principle component analysis (PCA)
For
more information about Jalview, look at http://www.ebi.ac.uk/jalview/
Why does Jalview not work
for me?
If
Jalview is not available with your results, this is because the program
requires that your browser supports Java applets (provided by Java runtime
plugin). To check that you have enabled Java applets go to Preferences,
Advanced, and "Enable Java".
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