ProValidator:
A tool to design and validate profiles for prokaryotic protein families
Help
-
Contact
Session: no session
Step 1: Manage sessions
Create a session is necessary to supervise the process in each step
:
- Click here to
create
a new session and asignate a session number:
- Or introduce your asignated session number to
manage
your session:
- Or click here to
close and delete
the active session:
(All data will be deleted. Sessions will expire in one week from the last change)
Step 2: Preparing profile seed
Sequences (in FASTA format -
example
):
| Similarity threshold (3-100):
% | Keyword for filtering:
Black list:
hypothetical
probable
putative
fragment
- After the seed of the profile is chosen, use an alignment program (
CLUSTALW
) in order to align this seed and choose a conserved region.
(Output format: MSF)
Step 3: Constructing profile
Alignment (in MSF format -
example
):
Limits:
Mode:
Global
Domain global
Semiglobal
Local
Calibrate profile (calibration can take 10-60 min, depending on profile length)
Step 4: Run the profile against database
Use last profile
- or -
Profile (
example
):
AGAINST:
UniProt Database (
UniProt version
)
- or -
Database (in FASTA):
(Running can take several hours, depending on profile length)
Step 5: Validate the profile
Your profile can be validated with InterPro only if it was run against UniProt (
InterPro version
)
Query form for InterPro entries and methods
InterPro ID:
(eg. IPR005471)
Signature of adquisition method (optional):
(eg. PF09339)
Cutoff score: