proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Rosenkranz, David ^a   Zischler, Hans ^a  

^a JOHANNES GUTENBERG UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMOUNT OF INFORMATION; CLUSTER DETECTION; IMPORTANT FEATURES; PROBABILISTIC TRACKING; SENSITIVITY AND SPECIFICITY; TRANSPOSABLE ELEMENTS; UNIFORM DISTRIBUTION; VISUALIZATION AND ANALYSIS;

BIOINFORMATICS; GENES; VISUALIZATION;

PROBABILITY DISTRIBUTIONS;

MACACA; METAZOA; RATTUS;

SMALL INTERFERING RNA;

ANIMAL; ARTICLE; COMPUTER PROGRAM; GENE LIBRARY; GENETICS; GENOMICS; HUMAN; ISOLATION AND PURIFICATION; METABOLISM; MOUSE; RAT; RNA INTERFERENCE; TRANSPOSON;

ANIMALS; DNA TRANSPOSABLE ELEMENTS; GENE LIBRARY; GENOMICS; HUMANS; MICE; RATS; RNA INTERFERENCE; RNA, SMALL INTERFERING; SOFTWARE;

EID: 84855505301     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-5     Document Type: Article

References (13)

1. Thomson T, Lin H. The biogenesis and function of PIWI proteins and piRNAs: progress and prospect. Annu Rev Cell Dev Biol 2009, 25:355-376. 10.1146/annurev.cellbio.24.110707.175327, 2780330, 19575643.
2. Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 2007, 128:1089-1103. 10.1016/j.cell.2007.01.043, 17346786.
3. Aravin AA, Sachidanandam R, Bourc'his D, Schaefer C, Pezic D, Fejes Toth K, Bestor T, Hannon GJ. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol Cell 2008, 31(6):785-799. 10.1016/j.molcel.2008.09.003, 2730041, 18922463.
4. Girard A, Sachidanandam R, Hannon GJ, Carmell MA. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 2006, 442:199-202.
5. Lau NC, Seto AG, Kim J, Kuramochi-Miyagawa S, Nakano T, Bartel DP, Kingston RE. Characterization of the piRNA complex from rat testes. Science 2006, 313:305-306. 10.1126/science.1131186, 16857925.
6. Assis R, Kondrashov AS. Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution. Proc Natl Acad Sci USA 2009, 17:7079-7082.
7. Lakshmi SS, Agrawal S. piRNABank: a web resource on classified and clustered Piwi-interacting RNAs. Nucleic Acids Res 2008, 36(Database issue):D173-D177. 2238943, 17881367.
8. Jiang H, Wong HW. SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 2008, 24:2395-2396. 10.1093/bioinformatics/btn429, 2562015, 18697769.
9. NCBI nucleotide database. , http://www.ncbi.nlm.nih.gov/nuccore
10. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 2005, 110(1-4):462-467. 10.1159/000084979, 16093699.
11. Batzer M, Deininger P. Alu repeats and human genomic diversity. Nat Rev Genet 2002, 3(5):370-379. 10.1038/nrg798, 11988762.
12. Grivna ST, Pyhtila B, Lin H. MIWI associates with translational machinery and PIWI-interacting RNAs (piRNAs) in regulating spermatogenesis. Proc Natl Acad Sci USA 2006, 103:13415-13420. 10.1073/pnas.0605506103, 1569178, 16938833.
13. Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N, Imai H. Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev 2006, 20(13):1732-1743. 10.1101/gad.1425706, 1522070, 16766679.