title: isomiR-SEA: an RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation.
abstract: BACKGROUND
  Massive parallel sequencing of transcriptomes, revealed the presence of many miRNAs and miRNAs variants named isomiRs with a potential role in several cellular processes through their interaction with a target mRNA. Many methods and tools have been recently devised to detect and quantify miRNAs from sequencing data. However, all of them are implemented on top of general purpose alignment methods, thus providing poorly accurate results and no information concerning isomiRs and conserved miRNA-mRNA interaction sites.
  
  
  RESULTS
  To overcome these limitations we present a novel algorithm named isomiR-SEA, that is able to provide users with very accurate miRNAs expression levels and both isomiRs and miRNA-mRNA interaction sites precise classifications. Tags are mapped on the known miRNAs sequences thanks to a specialized alignment algorithm developed on top of biological evidence concerning miRNAs structure. Specifically, isomiR-SEA checks for miRNA seed presence in the input tags and evaluates, during all the alignment phases, the positions of the encountered mismatches, thus allowing to distinguish among the different isomiRs and conserved miRNA-mRNA interaction sites.
  
  
  CONCLUSIONS
  isomiR-SEA performances have been assessed on two public RNA-Seq datasets proving that the implemented algorithm is able to account for more reliable and accurate miRNAs expression levels with respect to those provided by two compared state of the art tools. Moreover, differently from the few methods currently available to perform isomiRs detection, the proposed algorithm implements the evaluation of isomiRs and conserved miRNA-mRNA interaction sites already in the first alignment phases, thus avoiding any additional filtering stages potentially responsible for the loss of useful information.
authors.affiliation: Department of Control and Computer Engineering DAUIN, Politecnico di Torino,, C.so Duca degli Abruzzi 24, Turin, 10129, IT, Italy. gianvito.urgese@polito.it.
authors.forename: Gianvito
authors.initials: G
authors.lastname: Urgese
authors.affiliation: Department of Control and Computer Engineering DAUIN, Politecnico di Torino,, C.so Duca degli Abruzzi 24, Turin, 10129, IT, Italy.
authors.forename: Giulia
authors.initials: G
authors.lastname: Paciello
authors.affiliation: Department of Control and Computer Engineering DAUIN, Politecnico di Torino,, C.so Duca degli Abruzzi 24, Turin, 10129, IT, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Acquaviva
authors.affiliation: Department of Control and Computer Engineering DAUIN, Politecnico di Torino,, C.so Duca degli Abruzzi 24, Turin, 10129, IT, Italy.
authors.forename: Elisa
authors.initials: E
authors.lastname: Ficarra
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020407:Internet; D035683:MicroRNAs / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D016376:Oligonucleotides, Antisense / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D014584:User-Computer Interface
chemical_list: D035683:MicroRNAs; D016376:Oligonucleotides, Antisense; D012333:RNA, Messenger
keywords: Expression level; isomiR; miRNA; miRNA-mRNA interaction site