title: 3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments.
abstract: Protein-coding genes with multiple alternative polyadenylation sites can generate mRNA 3'UTR sequences of different lengths, thereby causing the loss or gain of regulatory elements, which can affect stability, localization and translation efficiency. 3USS is a web-server developed with the aim of giving experimentalists the possibility to automatically identify alternative 3 ': UTRs (shorter or longer with respect to a reference transcriptome), an option that is not available in standard RNA-seq data analysis procedures. The tool reports as putative novel the 3 ': UTRs not annotated in available databases. Furthermore, if data from two related samples are uploaded, common and specific alternative 3 ': UTRs are identified and reported by the server.
  
  
  METHODS
  3USS is freely available at http://www.biocomputing.it/3uss_server.
authors.affiliation: Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy.
authors.forename: Loredana
authors.initials: L
authors.lastname: Le Pera
authors.affiliation: Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy.
authors.forename: Mariagiovanna
authors.initials: M
authors.lastname: Mazzapioda
authors.affiliation: Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy.
authors.forename: Anna
authors.initials: A
authors.lastname: Tramontano
mesh_terms: D020413:3' Untranslated Regions; D020869:Gene Expression Profiling; D020407:Internet; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D020413:3' Untranslated Regions