title: SplamiR--prediction of spliced miRNAs in plants.
abstract: BACKGROUND
  MicroRNAs (miRNAs) are important regulators of biological processes in plants and animals. Recently, miRNA genes have been discovered, whose primary transcripts are spliced and which cannot be predicted directly from genomic sequence. Hence, more sophisticated programs for the detection of spliced miRNAs are required.
  
  
  RESULTS
  Here, we present the first method for the prediction of spliced miRNAs in plants. For a given genomic sequence, SplamiR creates a database of complementary sequence pairs, which might encode for RNAs folding into stem-loop structures. Next, in silico splice variants of database sequences with complementarity to an mRNA of interest are classified as to whether they could represent miRNAs targeting this mRNA. Our method identifies all known cases of spliced miRNAs in rice, and a previously undiscovered miRNA in maize which is supported by an expressed sequence tag (EST). SplamiR permits identification of spliced miRNAs for a given target mRNA in many plant genomes.
  
  
  BACKGROUND
  The program is freely available at http://www.uni-jena.de/SplamiR.html.
authors.affiliation: Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, Jena, Germany.
authors.forename: Christoph J
authors.initials: CJ
authors.lastname: Thieme
authors.forename: Lydia
authors.initials: L
authors.lastname: Gramzow
authors.forename: Dajana
authors.initials: D
authors.lastname: Lobbes
authors.forename: Günter
authors.initials: G
authors.lastname: Theissen
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics; D010944:Plants / Q000235:genetics*; D012326:RNA Splicing; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*; D017423:Sequence Analysis, RNA; D012984:Software; D003313:Zea mays / Q000235:genetics
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D018749:RNA, Plant