Check out the Quick guide to Zebra input and the Bioinformatic analysis of glutathione S-transferase superfamily for an example of the input and output data
Input data
Maximum file size: 50 MB
Allowed extensions: fasta fasta_aln
Maximum file size: 50 MB
Allowed extensions: fasta fasta_aln
Sequence ID to be used as a reference
Default: 1 (first sequence in the alignment file)
Leave the field blank to use default value
Apply offset to the reference sequence numbering
Default: 0
Leave the field blank to use default value
Threshold amount of gaps in a column
Default: 5%
Leave the field blank to use default value
Prediction of subfamily-specific positions
Number of random shuffles for each column
Default: 1000
Leave the field blank to use default value
Prediction of subfamily-specific positions: Optional input
Maximum file size: 10 MB
Allowed extensions: pdb
Maximum file size: 10 MB
Allowed extensions: pdb
Select protein chain
Leave the field blank to use the first chain
Maximum file size: 10 MB
Allowed extensions: pdb
Select protein chain
Leave the field blank to use the first chain
Select substrate and radius around it to define active site residues.
Default: <Empty> (not used)
Example: "ATP 10" (10Å around crystallographic ATP molecule)
Check this box to use 3D-mode
Radius to build list of neighbours
Default: 4 Å
Leave the field blank to use default value
Number of random shuffles for each column
Default: 1000
Leave the field blank to use default value
Functional subfamily classification
Amount of sequences allowed as outliers during clusterization
Default: 0.2
Example: value of '0.2' will make the program to accept classification with not more than 20% outliers compared to the sample size
Leave the field blank to use default value
Minimal number of sequences allowed in a subfamily
Default: 5% of the sample size if the field was left blank
Example: value of "3" will make the program to accept subfamilies with at least 3 sequences and larger (see explanation of Input for more details)
Leave the field blank to use default value
Minimal number of subfamilies
Default: 2
Leave the field blank to use default value
Max groups:
Maximum number of subfamilies
Default: 1000000000
Leave the field blank to use default value
Maximum file size: 10 MB
Allowed extensions: txt groupfile
Set a groupfile in txt format with definition of functional subfamilies (see explanation of Input for more details)