SFESA
(
S
hift to
F
ix secondary structure
E
lement
S
in
A
lignments)
A tool to refine
pairwise protein sequence alignment
, with a combination of
sequence and structural scoring
by
locally shifting secondary structure elements
.[
Documentation
]
Enter
query and template sequences in either of these formats
:
A pairwise alignment or
Two unaligned sequences
Or upload a file with sequences
Upload
a template (or template homolog) structure file
in
pdb format
(Strongly recommended)
Template structure file:
Or
enter PDB identifier
:
Chain:
Email address to receive the result (Recommended)
Job ID
(optional)
Submit
Choose
a SFESA alignment refinement mode
SFESA_O
SFESA_O+G
SFESA_O+G+M
SFESA_O+G+M+S
Parameters
Show/Hide
Identity threshold above which structure of template is applied:
Maximal residue positions to shift:
Non-gap threshold above which elements in template is appled SFESA:
Automatically assign structure for sequence in input
Yes
No
Advanced Parameters
Show/Hide
Parameters for generating Psi-blast profile:
Iterations
E-value
Identity cutoff below which distant homologs are removed
Documentation
Downloads
References:
Tong J, Pei J, Otwinowski Z, Grishin NV. "Refinement by shifting secondary structure elements improves sequence alignments."
Proteins. 2015 Mar;83(3):411-27. doi: 10.1002/prot.24746. Epub 2015 Jan 13.
Comments, suggestions and bug reports to
:
Last modified: Wed June 24 15:10:07 CDT 2015