Profile of Position Specific Scoring Matrix (PSSM)

This module allow user to generate normalized position specific scoring matrix for submitted protein or peptide sequence(s), where users are allowed to paste or upload file with multiple protein/peptide sequences [fasta format or single line sequences] similar to the Example sequence. The user can also provide the PDB or UniProt IDs in the mentioned format.

This module run PSI-BLAST in the backend with following parameters:
• Number of iteration = 3
• E-value = 1e-3
• Database = Swiss-Prot, User can download the database we used in the backend by clicking here.

If user want to calculate the PSSM using other parameters, kindly use standalone version of Pfeature, available at this here. For more information see HELP page.

Paste peptide sequence(s) in single line format or FASTA format:

OR Submit sequence file:

OR PDB IDs:

OR UniProt IDs:

Select portion of Sequence:

This section allow users to select either complete or specific portion of the seqeunce, such as

Whole: Performs operation on complete sequence
N-Term: This allows to cut the user specified portion from N-terminal of the sequence
C-Term: This allows to cut the user specified portion from C-terminal of the sequence
Split: This allows users to split the sequence into fragments and performs calculation indepedently
Rest: This allows users to drop the residues from N- and C-terminal and performs calculation on the remaining fragment

Whole N-Term C-Term Rest N-Term C-Term