PB-SVindex

Last update on Tuesday, March 20, 2018

Knowledge-based calculation of Structural Variability Indices (SVI) of pentapeptide sequences

This tool uses the knowledge of local conformations of pentapeptides in terms of PBs from PB-PENTAdb database to calculate a structural variability index (SVI) for each of them. It shows if a pentapeptide is observed to have multiple local conformations in terms of PBs or not.

This proposed index is similar to the Simpson’s diversity index used in population genetics :

pi is the fraction of all organisms which belong to the i-th species

Here we calculate SVI using an approximation of Simpson’s index :

where, for a given amino acid motif, ni is its occurence in PB class i, and n is the total number of times this motif is found in the database.
This is an estimator for Simpson’s index for sampling without replacement.

Assigned variability index values vary between 0 and 1. Lower values indicate sequences with low structural variability, higher values indicate higher structural variability.

PB-SVindex submission form

Provide your amino acid sequences in fasta format (max 1000 sequences) :

PB-SVI is currently under maintenance. We apologize for the inconvenience. It will be back soon.



As output, a table is provided with

  • first 8 characters of ID of sequence (it removes the “>” from first line),
  • SV index

with SVI values separated by comas.