FAQs

Table of Contents

  1. What is the primary purpose of this SWAKK web server?
  2. What is the difference between SWAKK and other similar web applications such as Consurf and Selecton?
  3. How long will my results be kept?
  4. Why do I get some error messages about my sequence?
  5. Why are there some amino acids (or codons) undetermined?
  1. What is the primary purpose of this SWAKK web server?

    To identify regions potentially under positive selection in proteins using a sliding window substituion analysis.

  2. What is the difference between SWAKK and other similar web applications such as Consurf and Selecton?

    We note that two important features distinguish our SWAKK server from other available web servers (15-17) that can identify functionally important sites in proteins. The first difference is that these other web servers focus on each single amino acid site or codon in the multiple sequence alignment, which essentially averages the overall time interval. Instead, our server considers a group of codons within a small window for each pair-wise comparison. Second, unlike other web servers where protein 3D structures are only used to display the results, our SWAKK server takes full advantage of the information intrinsically stored in a 3D structure to define neighboring codon groups. Without requiring an explicit evolutionary model or expensive computation, SWAKK thus provides a useful tool to complement the existing arsenal of methods for detecting positive selection.

  3. How long will my results be kept?

    Generally, results from each run will be kept for 14 days. Since the average running time is less than 30 second, you can always choose to run your analysis again.

  4. Why do I get some error messages about my sequence?

    This is either because your sequence contains some undefined symbols like X or N or ?, or because it is not a multiple times of three. You have to remove whole codons containing unknown symbols in order to make sure that the correct reading frame is maintained.

  5. 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 colored in yellow.