General input to Zebra
To use Zebra you have to submit
(1) a multiple alignment of proteins in the FASTA format and
(2) a representative protein (i.e., the query) structure in the PDB format
which should correspond to one of the proteins in the multiple alignment.
This input can be prepared automatically based on your query protein by the Mustguseal web-server via a web-interface (see below).
Bioinformatic analysis using Zebra and Mustguseal in four simple steps
(click here for an illustrated guide)
Step 1: Choose the query protein.
Choose the query protein based on your particular task and primary interest.
It can be the target protein selected for the further experimental design, the most studied member of the superfamily,
or a protein which you are the most familiar with.
Step 2: Automatically construct a large alignment of diverse protein families.
Press the "Mustguseal in NOW" button in the "The multiple protein alignment" box below. This will redirect you to the
Mustguseal web-server and load a preselected set of parameters (i.e., the Scenario 2).
Mustguseal can automatically construct large structure-based sequence alignments of thousands of proteins based on all available
information about their structures and sequences in public databases.
Enter the PDB ID and chain ID of your query protein in the "Query protein" box and press "Submit" to automatically construct
a large structure-guided sequence alignment of proteins with high structural but low sequence similarity to your query protein.
Step 3: Automatically transfer your data from Mustguseal to Zebra.
At the Mustguseal's "Results" page scroll down and press the "Submit to Zebra2" button. This will automatically transfer
the collected sequence and structural data to Zebra.
Step 4: Start Zebra.
Press "Submit" button to start the Zebra routine. When your task is processed, press "Results" to access the results and the
download section, and press "Analysis" to load the interactive on-line analysis tools.
Useful links:
