Sliding Window Analysis of KA and KS Web Server
Frequently Asked Questions
1. What is the primary purpose of this SWAKK web server?
To identify the regions potentially under positive selection using a sliding window substituion analysis.
2. What is difference between SWAKK and other similar web server such as Consurf and Selecton?
We note that there are two important features distinguishing our SWAKK server from currently existing web servers that identify functionally important sites in proteins. The first difference is that other web servers focus on each single amino acid site or codon in the multiple sequence alignment, which essentially averages the overall time interval. Yet, our server considers a group of codons within a small-size window at each time in the pair-wise comparison. Second, unlike other web servers where protein 3D structures are used only for the displaying purpose, our SWAKK server takes full advantage of information intrinsically stored in the 3D structure to define neighbor codon groups. Without requiring explicit evolutionary models or expensive computation, SWAKK thus works as a useful tool complementary to the existing ones.
3. Why I can not see the results in 3D view after a SWAKK run?
The first thing you should check is whether you have installed Chime plug-in in your computer. For troubleshooting, please read the link.
4. How long will my results be kept?
Generally, results from each run will be kept for one month. Since the average running time is less than 1 minute, you can always choose to run the analysis again.
5.Why do I get some error messages about my sequence?
This is either because your sequence contain some undefined symbols like X or N or ?, or because it is not the multiple times of three. You have to remove the whole codons containing unknown symbols in order to make sure that the correct reading frame is maintained.
6.Why are there some amino acids (or codons) undetermined?
Some amino acids in the structure have no corresponding codons in the alignment. These positions are undetermined and coloure as yellow.
If you have any questions about this web server, please email Han Liang at the University of Chicago.
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