Swelfe

A tool to detect internal repeats in DNA and amino acid sequences and in 3D structures

Introduction

Swelfe is a program that enables you to find internal repeats in DNA sequences, amino-acid sequences or 3D structures.
Several proteins have evolved by internal duplication. Looking for internal repeats is a good way to find these duplications.
As sequences evolve faster than 3D structures, older repeats can only be found in structures.
Swelfe can tell you if your protein contain repeat(s) and at which levels this/these repeat(s) can be found.

How to use Swelfe ?

You have to choose/specify a DNA or protein sequence or a 3D protein structure. Default parameter values are tuned for standard requests, but can be modified. Click on items for help.
You can download the program and have access to more functionalities (run on several sequences or 3D structures, more parameters)
If you need some help.
Acknowledgement
Reference

Structure input

or

Sequence input

upload a PDB file

    3D structures :

upload a fasta file

    DNA or amino acid ?:

or enter a PDB id

(important: consider specifying the chain - e.g. "1b7fA")

    3D structures or 3 levels ?:

or paste a fasta sequence

    DNA or amino acid ?:


 

Optional parameters

For DNA sequences, you can choose only one parameter
For amino acid sequences, you can choose up to two parameters (the matrix and another parameter)
For 3D structures, you can choose up to two parameters (the RRMSD and another parameter)
Parameters by default : For structure : RRMSD < 0.5 and score > 350 ;
For sequence : p-value < 0.01 ; For amino acid sequence : matrix BLOSUM62

Default parameters  

   Maximum Relative RMSd :  (only for structures)

Minimum score : 

Number of repeats : 

Minimum length of repeats : 

    Matrix :  (only for amino acid sequences)

P-value :  (only for sequences)

   P-value to have a repeat by chance (significant p-values are close to 0)

Other parameters

Gap opening penalty : 

Gap extension penalty : 

 Default for structure : opening 200 extension 50
Default for DNA sequence : opening 4 extension 1
Default for amino acid sequence : opening 8 extension 3

Remove overlapping repeats (ratio of overlap allowed) : 


 

For any question or problem, you can send an email to Anne-Laure Abraham:

This work was supported by grants from Region Ile-de-France and ACI IMPBIO 2003 Evolrep Project

Swelfe is hosted by RPBS