Erpin Home

Latest versions

erpin5.5.4.serv.tar.gz: Erpin distribution.
ErpinBatch.1.4.tar.gz: Batch Erpin execution file including all RFAM 9.1 and in-house alignments + Erpin Linux binaries. Read file manual.txt. Script for automatic generation of Erpin commands.


June 02 2011 :
Version 5.4. Bug fix: files with over 2Gb of sequence are now read correctly.
April 20 2009 :
New ErpinBatch archive (V1.4) here with ability to search RFAM9.1 almost in full (>1400 alignments).
June 6 2008 :
The "Erpinstandalone" distrib that contains Erpin+all RFAM datasets+all commands is renamed as "erpinbatch" to reduce confusion .
June 6 2008 :
New file.
Apr 14 2008 :
Find all ncRNAs in your favorite genome. Get the new Erpin batch script (tar.gz, includes all RFAM 8.1 and in-house alignments).
Jui 4 2007 :
The Erpin server is available in Orsay (in development).
Jan 13 2007 :
The Erpin home page has moved to Institut de Génétique et Microbiologie, Université Paris-Sud, Orsay
Online search is still in Marseille, here
Dec 15 2006 :
New Perl Script now generates a command line automatically based on a .epn alignment file.  See

Current Erpin version : 5.5 (download)

What is ERPIN ?

ERPIN (Easy RNA Profile IdentificatioN) is an RNA motif search program developped by Daniel Gautheret and André Lambert. Unlike most RNA pattern matching programs, ERPIN does not require users to write complex descriptors before starting a search. Instead ERPIN reads a sequence alignement and secondary structure, and automatically infers a statistical "secondary structure profile" (SSP). An original Dynamic Programming algorithm then matches this SSP onto any target database, finding solutions and their associated scores. In the latest version (unpublished) Erpin computes E-values for matches.

Please cite : Gautheret D, Lambert A. (2001) Direct RNA Motif Definition and Identification from Multiple Sequence Alignments using Secondary Structure Profiles. J Mol Biol. 313:1003-11 (abstract).


  • Funding : Logo IMPBIO

    Since July 2004, The ERPIN Web server  is funded by the French Ministry of Research through an ACI-IMPBIO fund. See the SERPIN home page (in french).

  • Web pages :

    J.-F. Fontaine 2003/2004
    S. Badi 2003

  • Search engine :

    JF.Fontaine 2003/2004
    G.Salin 2002