AdaPatch is a method for detecting positively selected patches of sites on the surface of viral proteins, which are likely candidates for being relevant for adaptive evolution.

Please upload your coding sequences as a multiple fasta file, and structural information as a PDB file with a chain identifier and a single amino acid sequence used to calculate surface accessibility of residues on the protein structure. Optionally, you can provide also a tree file, a NetSurfP file with surface accessibility values.

In the end patches under positive selection on the given protein structure will be visualized.

 
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Sequence input data:

Please provide a fasta file containing amino acid sequences:

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Please provide a fasta file containing corresponding coding sequences:

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Please provide a corresponding tree file (nexus format):

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Structure input data:

Please provide a NetsurfP file providing information on surface accessibility of residues:

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Please provide a fasta file holding the sequence used for prediction of surface accessibility:

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Please provide a corresponding PDB structure file:

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Please provide the ID of a corresponding PDB structure file:

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Please name the relevant chain identifier:

 
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Reference numbering:

Do you want to use a special amino acid sequence for reference numbering? If so, please provide a fasta file containing that sequence:

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Do you want a specific numbering relative to the reference sequence? If so, please provide an adequate numbering file.

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