title: The sufficient minimal set of miRNA seed types.
abstract: BACKGROUND
  Pairing between the target sequence and the 6-8 nt long seed sequence of the miRNA presents the most important feature for miRNA target site prediction. Novel high-throughput technologies such as Argonaute HITS-CLIP afford meanwhile a detailed study of miRNA:mRNA duplices. These interaction maps enable a first discrimination between functional and non-functional target sites in a bulky fashion. Prediction algorithms apply different seed paradigms to identify miRNA target sites. Therefore, a quantitative assessment of miRNA target site prediction is of major interest.
  
  
  RESULTS
  We identified a set of canonical seed types based on a transcriptome wide analysis of experimentally verified functional target sites. We confirmed the specificity of long seeds but we found that the majority of functional target sites are formed by less specific seeds of only 6 nt indicating a crucial role of this type. A substantial fraction of genuine target sites arenon-conserved. Moreover, the majority of functional sites remain uncovered by common prediction methods.
authors: Institute of Bioinformatics and Systems Biology (MIPS), Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
authors: Daniel C
authors: DC
authors: Ellwanger
authors: Florian A
authors: FA
authors: Büttner
authors: Hans-Werner
authors: HW
authors: Mewes
authors: Volker
authors: V
authors: Stümpflen
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D039642:Eukaryotic Initiation Factors / Q000378:metabolism; D020869:Gene Expression Profiling; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D009841:Oligonucleotides / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism
chemical_list: D039642:Eukaryotic Initiation Factors; D035683:MicroRNAs; D009841:Oligonucleotides; D012333:RNA, Messenger