title: piRNAQuest: searching the piRNAome for silencers.
abstract: BACKGROUND
  PIWI-interacting RNA (piRNA) is a novel and emerging class of small non-coding RNA (sncRNA). Ranging in length from 26-32 nucleotides, this sncRNA is a potent player in guiding the vital regulatory processes within a cellular system. Inspite of having such a wide role within cellular systems, piRNAs are not well organized and classified, so that a researcher can pool out the biologically relevant information concerning this class.
  
  
  METHODS
  Here we present piRNAQuest- a unified and comprehensive database of 41749 human, 890078 mouse and 66758 rat piRNAs obtained from NCBI and different small RNA sequence experiments. This database provides piRNA annotation based on their localization in gene, intron, intergenic, CDS, 5/UTR, 3/UTR and repetitive regions which has not been done so far. We have also annotated piRNA clusters and have elucidated characteristic motifs within them. We have looked for the presence of piRNAs and piRNA clusters in pseudogenes, which are known to regulate the expression of protein coding transcripts by generating small RNAs. All these will help researchers progress towards solving the unanswered queries on piRNA biogenesis and their mode of action. Further, expression profile for piRNA in different tissues and from different developmental stages has been provided. In addition, we have provided several tools like 'homology search', 'dynamic cluster search' and 'pattern search'. Overall, piRNAQuest will serve as a useful resource for exploring human, mouse and rat piRNAome. The database is freely accessible and available at http://bicresources.jcbose.ac.in/zhumur/pirnaquest/.
  
  
  CONCLUSIONS
  piRNAs play a remarkable role in stem cell self-renewal and various vital processes of developmental biology. Although researchers are mining different features on piRNAs, the exact regulatory mechanism is still fuzzy. Thus, understanding the true potential of these small regulatory molecules with respect to their origin, localization and mode of biogenesis is crucial. piRNAQuest will provide us with a better insight on piRNA origin and function which will help to explore the true potential of these sncRNAs.
authors.forename: Arijita
authors.initials: A
authors.lastname: Sarkar
authors.forename: Ranjan Kumar
authors.initials: RK
authors.lastname: Maji
authors.forename: Sudipto
authors.initials: S
authors.lastname: Saha
authors.affiliation: Bioinformatics Centre, Bose Institute, Kolkata 700054, India. zhumur@jcbose.ac.in.
authors.forename: Zhumur
authors.initials: Z
authors.lastname: Ghosh
mesh_terms: D000818:Animals; D004251:DNA Transposable Elements; D030561:Databases, Nucleic Acid; D006801:Humans; D051379:Mice; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000145:classification / Q000235:genetics*; D051381:Rats; D012091:Repetitive Sequences, Nucleic Acid; D059467:Transcriptome
chemical_list: D004251:DNA Transposable Elements; D034741:RNA, Small Interfering