Zebra: a web-server for bioinformatic analysis of
subfamily-specific and conserved positions in diverse protein superfamilies


Version 2.0

Choose input mode

Mode 1: Submit a multiple sequence alignment of a protein family/superfamily and a 3D-structure of the representative protein
Mode 2: Submit only a multiple sequence alignment of a protein family/superfamily
Claim your results by TaskID (access the results and progress log of a previously submitted task)
Submit a multiple protein alignment and a representative protein structure as a new task, or access a previous submission by TaskID

Submit a new task


The multiple protein alignment

Upload a file with a multiple protein alignment in fasta format. File size must not exceed 100 MB. File extention must be "fasta" or "fasta_aln". E.g.: file.fasta_aln.
No alignment? Press to run the Mustguseal web-server with a pre-selected set of parameters and automatically construct a multiple alignment of your protein families for further analysis by the Zebra.
The representative protein structure

Upload a file with protein structure in the PDB format. File size must not exceed 10 MB. File extention must be "pdb". E.g.: filename.pdb.
Enter a case sensitive chain ID (e.g., 'A' to select chain A) or 'first' to select the first chain in the uploaded file.
Enter a positive integer (e.g., '10' to select the 10-th protein in the alignment to match the protein structure) or 'auto' to select the best match automatically
Security and sharing
No Yes

No Yes

Zebra options: general
Consider all columns
Select columns by residues around a ligand in PDB
Select columns by column ID
Enter an integer (e.g., '5' to set the threshold to 5% from the total number of proteins in the alignment)
Zebra options: statistical significance
Enter an integer ≤10000 (e.g., '1000' to shuffle each column 1000 times)
Zebra options: 3D-mode
Enter a floating-point number (e.g., '4' to select all neighbors within 4 Angstroms or '0' to deactivate)
Zebra options: classification into subfamilies
Zebra CD-HIT Manual
Enter an integer (e.g., '5' to consider classifications with at least 5 subfamilies) or 'auto' for automatic
Enter an integer (e.g., '10' to consider classifications with at most 10 subfamilies) or 'auto' for automatic
Enter an integer within a range [0; 100) (e.g., '20' to consider classifications with at most 20% outliers from the total number of proteins in the multiple alignment)
Enter an integer within a range [0; 50] (e.g., '5' to consider only subfamilies with at least 5% proteins from the total number of proteins in the multiple alignment, or '0' to consider all subfamilies with at least 3 proteins)