title: The ERPIN server: an interface to profile-based RNA motif identification.
abstract: ERPIN is an RNA motif identification program that takes an RNA sequence alignment as an input and identifies related sequences using a profile-based dynamic programming algorithm. ERPIN differs from other RNA motif search programs in its ability to capture subtle biases in the training set and produce highly specific and sensitive searches, while keeping CPU requirements at a practical level. In its latest version, ERPIN also computes E-values, which tell biologists how likely they are to encounter a specific sequence match by chance-a useful indication of biological significance. We present here the ERPIN online search interface (http://tagc.univ-mrs.fr/erpin/). This web server automatically performs ERPIN searches for different RNA genes or motifs, using predefined training sets and search parameters. With a couple of clicks, users can analyze an entire bacterial genome or a genomic segment of up to 5Mb for the presence of tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and other motifs. Search results are displayed with sequence, score, position, E-value and secondary structure graphics. An example of a complete genome scan is provided, as well as an evaluation of run times and specificity/sensitivity information for all available motifs.
authors.affiliation: CNRS UMR 6207, Université de la Méditerranée, Luminy Case 906, 13288 Marseille, Cedex 09, France.
authors.forename: André
authors.initials: A
authors.lastname: Lambert
authors.forename: Jean-Fred
authors.initials: JF
authors.lastname: Fontaine
authors.forename: Matthieu
authors.initials: M
authors.lastname: Legendre
authors.forename: Fabrice
authors.initials: F
authors.lastname: Leclerc
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Permal
authors.forename: François
authors.initials: F
authors.lastname: Major
authors.forename: Harald
authors.initials: H
authors.lastname: Putzer
authors.forename: Olivier
authors.initials: O
authors.lastname: Delfour
authors.forename: Bernard
authors.initials: B
authors.lastname: Michot
authors.forename: Daniel
authors.initials: D
authors.lastname: Gautheret
mesh_terms: D020407:Internet; D038621:Regulatory Sequences, Ribonucleic Acid; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012984:Software; D014584:User-Computer Interface
chemical_list: D038621:Regulatory Sequences, Ribonucleic Acid