NucBase, an easy to use read mapper for small RNAs

Mobile DNA

Volumn 4, Issue 1, 2013, Pages

  Dufourt, Jeremy ^a,b,c   Pouchin, Pierre ^a,b,c,d   Peyret, Pierre ^a   Brasset, Emilie ^a,b,c   Vaury, Chantal ^a,b,c  

^a UNIVERSITÉ CLERMONT AUVERGNE   (France)

^b INSERM   (France)

^c CNRS   (France)

^d UNIVERSITY HOSPITAL OF CLERMONT FERRAND   (France)

Author keywords

Alignment; Short reads

Indexed keywords

RNA;

ARTICLE; COMPUTER PROGRAM; GENE SEQUENCE; GENETIC DATABASE; PRIORITY JOURNAL; RNA SEQUENCE; TRANSPOSON;

EID: 84873021909     PISSN: None     EISSN: 17598753     Source Type: Journal    
DOI: 10.1186/1759-8753-4-1     Document Type: Article

References (17)

1. Sequencing technologies-the next generation. Metzker ML, Nat Rev Genet 2010 11 31 46 10.1038/nrg2626 19997069
2. Biogenesis of small RNAs in animals. Kim VN, Han J, Siomi MC, Nat Rev Mol Cell Biol 2009 10 126 139 10.1038/nrm2632 19165215
3. In Drosophila melanogaster the COM locus directs the somatic silencing of two retrotransposons through both Piwi-dependent and -independent pathways. Desset S, Buchon N, Meignin C, Coiffet M, Vaury C, PLoS One 2008 3 1526 10.1371/journal.pone.0001526 18253480 (Pubitemid 351836688)
4. MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Carmell MA, Girard A, van de Kant HJ, Bourc'his D, Bestor TH, de Rooij DG, Hannon GJ, Dev Cell 2007 12 503 514 10.1016/j.devcel. 2007.03.001 17395546 (Pubitemid 46523643)
5. A novel class of small RNAs bind to MILI protein in mouse testes. Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P, Iovino N, Morris P, Brownstein MJ, Kuramochi-Miyagawa S, Nakano T, Chien M, Russo JJ, Ju J, Sheridan R, Sander C, Zavolan M, Tuschl T, Nature 2006 442 203 207 16751777 (Pubitemid 44086567)
6. A germline-specific class of small RNAs binds mammalian Piwi proteins. Girard A, Sachidanandam R, Hannon GJ, Carmell MA, Nature 2006 442 199 202 16751776 (Pubitemid 44086566)
7. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ, Cell 2007 128 1089 1103 10.1016/j.cell.2007.01.043 17346786 (Pubitemid 46427877)
8. An epigenetic role for maternally inherited piRNAs in transposon silencing. Brennecke J, Malone CD, Aravin AA, Sachidanandam R, Stark A, Hannon GJ, Science 2008 322 1387 1392 10.1126/science.1165171 19039138 (Pubitemid 352775252)
9. SOAP: short oligonucleotide alignment program. Li R, Li Y, Kristiansen K, Wang J, Bioinformatics 2008 24 713 714 10.1093/bioinformatics/btn025 18227114 (Pubitemid 351321217)
10. Fast and accurate long-read alignment with Burrows-Wheeler transform. Li H, Durbin R, Bioinformatics 2010 26 589 595 10.1093/bioinformatics/btp698 20080505
11. Fast gapped-read alignment with Bowtie 2. Langmead B, Salzberg SL, Nat Methods 2012 9 357 359 10.1038/nmeth.1923 22388286
12. REPuter: the manifold applications of repeat analysis on a genomic scale. Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R, Nucleic Acids Res 2001 29 4633 4642 10.1093/nar/29.22.4633 11713313 (Pubitemid 33095024)
13. Burrows M, Wheeler DJ, A Block Sorting Lossless Data Compression Algorithm Digital Equipment Corporation: Palo Alto, CA Technical Report 124. 1994
14. Opportunistic Data Structures with Applications. Proceedings of the 41st Annual Symposium on Foundations of Computer Science. Ferragina P, Manzini G, IEEE Computer Society 2000 390
15. Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment. Ferragina P, Giancarlo R, Greco V, Manzini G, Valiente G, BMC Bioinformatics 2007 8 252 10.1186/1471-2105-8-252 17629909 (Pubitemid 47226311)
16. Approximate Pattern Matching using the Burrows-Wheeler Transform. Zhang N, Mukherjee A, Adjeroh DA, Bell T, DCC. IEEE Computer Society 2003 458
17. Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo. Rouget C, Papin C, Boureux A, Meunier AC, Franco B, Robine N, Lai EC, Pelisson A, Simonelig M, Nature 2010 467 1128 1132 10.1038/nature09465 20953170