Sliding Window Analysis of KA and KS Web Server

Help

 

 

Input:

Structure

Currently, SWAKK only accepts the structure in the PDB File Format.

To run SWAKK you should specify a Chain Identifier (A, B, C, in the corresponding field of the PDB file). Amino acids in the irrelevant chains keeps their orignial colours in the results, so it is recommended that only the relevant structure is uploaded as the input.

You can find the chain identifiers of a standard PDB file on the third field (column 12) of the SEQRES records or the sixth field (column 22) of the ATOM records. The chain identifier may be any single legal character, including a blank character, which is used if there is only one chain.

For more information check the PDB File Format Contents Guide.

Sequences

You can either upload sequence files in fasta format or paste sequences directly ( the title line is not required.) Sequences could be in lower or capital letters. When the sequence is too long, file uploading is recommended.

Currently only standard nucleotide symbols (A, T , U, G and C) are acceptable. All the other symbols like X or ? should be removed from the sequences. You have to make it sure that your sequences are in the correct reading frames before submitting them.

Advanced Option

This is the cut-offs of KA/KS that you choose to color the molecule.

Graphic Visualization

The results are displayed in 3D space, which needs Chime plug-in. The version works both in Internet Explorer (starting from version IE5.5 SP2 with Chime 2.6 SP3) and? Netscape Communicator (version 4.7x).

You can click the right button in the mouse to move the molecule and choose different display styles.

If you have any questions about this web server, please email Han Liang at the University of Chicago.

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