Secondary Structure Annotation

This module allow users to predict regular secondary structure in their protein. Basically secondary structures are assigned in a query protein based on its similarity with known protein structure in PDB. This module allow users to select desired BLAST parameters for performing similarity search. Advanced option further facilitate users in selecting most appropriate parameters. There are three non-redundant database againt which BLAST can be performed: 40%, 70% and 100%. The secondary structure information is displayed according to DSSP defination. User can select whether to perform annotation based on eight DSSP states or standard three states. In order to obtain more information on secondary structure states of DSSP Click here.

Sequence Submission Form

Paste your Protein sequence in FASTA format (single sequence only)

Select number of top BLAST hits for annotation:        Expect Value (e-value):        Weight Matrix:


 Select level of redundancy  40%  70%  100%
   
 Select secondary structure states  Eight DSSP state
[H,G,I,B,E,T,S,C]		  Standard 3-states
[H=(G,H,I); E=(B,E); C=(T,S)]