DSAP: Deep-sequencing small RNA analysis pipeline

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Huang, Po Jung ^a,b   Liu, Yi Chung ^a   Lee, Chi Ching ^a   Lin, Wei Chen ^b   Gan, Richie Ruei Chi ^b   Lyu, Ping Chiang ^a   Tang, Petrus ^b  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^b CHANG GUNG UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RNA; UNTRANSLATED RNA;

ARTICLE; AUTOMATION; BIOINFORMATICS; CHICKEN; CLIENT SERVER APPLICATION; GENE EXPRESSION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; SPECIES COMPARISON; CHEMISTRY; COMPUTER PROGRAM; INTERNET; METABOLISM; SEQUENCE ANALYSIS;

INTERNET; MICRORNAS; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 77954304695     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq392     Document Type: Article

References (31)

1. Brennecke, J., Hipfner, D.R., Stark, A., Russell, R.B. and Cohen, S.M. (2003) bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell, 113, 25-36.
2. Carrington, J.C. and Ambros, V. (2003) Role of microRNAs in plant and animal development. Science, 301, 336-338.
3. Chen, C.Z., Li, L., Lodish, H.F. and Bartel, D.P. (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science, 303, 83-86.
4. Cheng, A.M., Byrom, M.W., Shelton, J. and Ford, L.P. (2005) Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis. Nucleic Acids Res., 33, 1290-1297.
5. Lee, R.C., Feinbaum, R.L. and Ambros, V. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75, 843-854.
6. Reinhart, B.J., Slack, F.J., Basson, M., Pasquinelli, A.E., Bettinger, J.C., Rougvie, A.E., Horvitz, H.R. and Ruvkun, G. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature, 403, 901-906.
7. Bartel, D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
8. Borchert, G.M., Lanier, W. and Davidson, B.L. (2006) RNA polymerase III transcribes human microRNAs. Nat. Struct. Mol. Biol., 13, 1097-1101.
9. Du, T. and Zamore, P.D. (2005) microPrimer: the biogenesis and function of microRNA. Development, 132, 4645-4652.
10. Lee, Y., Kim, M., Han, J., Yeom, K.H., Lee, S., Baek, S.H. and Kim, V.N. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J., 23, 4051-4060.
11. Zeng, Y., Yi, R. and Cullen, B.R. (2005) Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J., 24, 138-148.
12. Schwarz, D.S., Hutvagner, G., Du, T., Xu, Z., Aronin, N. and Zamore, P.D. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell, 115, 199-208.
13. Gardner, P.P., Daub, J., Tate, J.G., Nawrocki, E.P., Kolbe, D.L., Lindgreen, S., Wilkinson, A.C., Finn, R.D., Griffiths-Jones, S., Eddy, S.R. et al. (2009) Rfam: updates to the RNA families database. Nucleic Acids Res., 37, D136-D140.
14. Griffiths-Jones, S. (2005) Annotating non-coding RNAs with Rfam. Curr. Protoc. Bioinformatics, Chapter 12, Unit 12 15.
15. Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A. and Eddy, S.R. (2003) Rfam: an RNA family database. Nucleic Acids Res., 31, 439-441.
16. Griffiths-Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S.R. and Bateman, A. (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res., 33, D121-D124.
17. Griffiths-Jones, S. (2006) miRBase: the microRNA sequence database. Methods Mol. Biol., 342, 129-138.
18. Pavlidis, P. and Noble, W.S. (2003) Matrix2png: a utility for visualizing matrix data. Bioinformatics, 19, 295-296.
19. Mullan, L.J. and Bleasby, A.J. (2002) Short EMBOSS user guide. European molecular biology open software suite. Brief. Bioinformatics, 3, 92-94.
20. Olson, S.A. (2002) EMBOSS opens up sequence analysis. European molecular biology open software suite. Brief. Bioinformatics, 3, 87-91.
21. Rice, P., Longden, I. and Bleasby, A. (2000) EMBOSS: the European molecular biology open software suite. Trends Genet., 16, 276-277.
22. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
23. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
24. Glazov, E.A., Cottee, P.A., Barris, W.C., Moore, R.J., Dalrymple, B.P. and Tizard, M.L. (2008) A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res., 18, 957-964.
25. Kuchenbauer, F., Morin, R.D., Argiropoulos, B., Petriv, O.I., Griffith, M., Heuser, M., Yung, E., Piper, J., Delaney, A., Prabhu, A.L. et al. (2008) In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res., 18, 1787-1797.
26. Moretti, S., Wilm, A., Higgins, D.G., Xenarios, I. and Notredame, C. (2008) R-Coffee: a web server for accurately aligning noncoding RNA sequences. Nucleic Acids Res., 36, W10-W13.
27. Thompson, J.D., Gibson, T.J. and Higgins, D.G. (2002) Multiple sequence alignment using ClustalW and ClustalX. Curr. Protoc. Bioinformatics, Chapter 2, Unit 2 3.
28. Wilm, A., Higgins, D.G. and Notredame, C. (2008) R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res., 36, e52.
29. Hackenberg, M., Sturm, M., Langenberger, D., Falcon-Perez, J.M. and Aransay, A.M. (2009) miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res., 37, W68-W76.
30. Wang, W.C., Lin, F.M., Chang, W.C., Lin, K.Y., Huang, H.D. and Lin, N.S. (2009) miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics, 10, 328.
31. Friedlander, M.R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S. and Rajewsky, N. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol., 26, 407-415.