RNAstrand: Reading direction of structured RNAs in multiple sequence alignments

Algorithms for Molecular Biology

Volumn 2, Issue 1, 2007, Pages

  Reiche, Kristin ^a   Stadler, Peter F ^a,b,c  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b UNIVERSITY OF VIENNA   (Austria)

^c SANTA FE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MAMMALIA; NEMATODA;

EID: 34250783658     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-2-6     Document Type: Article

References (28)

1. Washietl S Hofacker IL Stadler PF Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome Nat Biotechnol 2005 23 11 1383-1390 10.1038/nbt1144 16273071
2. Pedersen JS Bejerano G Siepel A Rosenbloom K Lindblad-Toh K Lander ES Kent J Miller W Haussler D Identification and Classification of Conserved RNA Secondary Structures in the Human Genome PLoS Comput Biol 2006 2 4 e33 10.1371/journal.pcbi.0020033 16628248 1440920
3. Washietl S Pedersen JS Korbel JO Gruber A Hackermüller J Hertel J Lindemeyer M Reiche K Stocsits C Tanzer A Ucla C Wyss C Antonarakis SE Denoeud F Lagarde J Drenkow J Kapranov P Gingeras TR Guigó R Snyder M Gerstein MB Reymond A Hofacker IL Stadler PF Structured RNAs in the ENCODE Selected Regions of the Human Genome Gen Res 2007
4. Missal K Rose D Stadler PF Non-coding RNAs in Ciona intestinalis Bioinformatics 2005 21 Suppl 2 ii77-ii78 10.1093/bioinformatics/bti1113 16204130
5. Missal K Zhu X Rose D Deng W Skogerbø G Chen R Stadler PF Prediction of Structured Non-Coding RNAs in the Genome of the Nematode Caenorhabitis elegans J Exp Zoolog B Mol Dev Evol 2006 306 4 379-392 10.1002/jez.b.21086 16425273
6. Rose DR Hackermüller J Washietl S Findeiß S Reiche K Hertel J Stadler PF Prohaska SJ Computational RNomics of Drosophilids BMC Genomics 2007
7. Kapranov P Cheng J Dike S Nix D Duttagupta R Willingham AT Stadler PF Hertel J Hackermüller J Hofacker IL Bell I Cheung E Drenkow J Dumais E Patel S Helt G Madhavan G Piccolboni A Sementchenko V Tammana H Gingeras TR RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription Science 2007 17510325
8. Cristianini N Shawe-Taylor J An Introduction to Support Vector Machines Cambridge UK: Cambridge University Press 2000
9. Mathews DH Sabina J Zuker M Turner H Expanded Sequence Dependence of Thermodynamic Parameters Provides Robust Prediction of RNA Secondary Structure J Mol Biol 1999 288 911-940 10329189 10.1006/jmbi.1999.2700
10. Lu ZJ Turner DH Mathews DH A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation Nucleic Acids Res 2006 34 4912-4924 16982646 10.1093/nar/gkl472 1635246
11. Hofacker IL Fekete M Stadler PF Secondary Structure Prediction for Aligned RNA Sequences J Mol Biol 2002 319 1059-1066 12079347 10.1016/ S0022-2836(02)00308-X
12. Doshi KJ Cannone JJ Cobaugh CW Gutell RR Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction BMC Bioinformatics 2004 5 105 15296519 10.1186/1471-2105-5-105 514602
13. Carter RJ Dubchak I Holbrook SR A computational approach to identify genes for functional RNAs in genomic sequences Nucl Acids Res 2001 29 19 3928-3938 60242 11574674
14. Hofacker IL Fontana W Stadler PF Bonhoeffer LS Tacker M Schuster P Fast Folding and Comparison of RNA Secondary Structures Monatsh Chem 1994 125 167-188 10.1007/BF00818163
15. Washietl S Hofacker IL Stadler PF Fast and reliable prediction of noncoding RNAs Proc Natl Acad Sci USA 2005 102 2454-2459 15665081 10.1073/pnas.0409169102 548974
16. Gardner PP Wilm A Washietl S A benchmark of multiple sequence alignment programs upon structural RNAs Nucl Acids Res 2005 33 2433-2439 15860779 10.1093/nar/gki541 1087786
17. Washietl S rnazWindow.pl http://www.tbi.univie.ac.at/~wash/RNAz/man/ rnazWindow.html
18. Chang CC Lin CJ LIBSVM: A library for support vector machines 2001 http://www.csie.ntu.edu.tw/~cjlin/libsvm
19. Youden WJ Index for rating diagnostic tests Cancer 1950 3 32-35 15405679 10.1002/1097-0142(1950)3:1<32::AID-CNCR2820030106>3.0.CO;2-3
20. Liu C Bai B Skogerbœ G Cai L Deng W Zhang Y Bu D Zhao Y Chen R NONCODE: An integrated knowledge database of non-coding RNAs Nucleic Acids Res 2005 33 D112-D115 15608158 10.1093/nar/gki041 539995
21. Griffiths-Jones S Moxon S Marshall M Khanna A Eddy SR Bateman A Rfam: annotating non-coding RNAs in complete genomes Nucleic Acids Res 2005 33 D121-D124 15608160 10.1093/nar/gki081 540035
22. Griffiths-Jones S The microRNA Registry Nucl Acids Res 2004 32 D109-D111 14681370 10.1093/nar/gkh023 308757
23. Lestrade L Weber MJ snoRNA-LBME-db, a comprehensive database of human H/ ACA and C/D box snoRNAs Nucleic Acids Research 2006 34 D158-D162 16381836 10.1093/nar/gkj002 1347365
24. The ENCODE Project Consortium Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 2007
25. Fontana W Stadler PF Bornberg-Bauer EG Griesmacher T Hofacker IL Tacker M Tarazona P Weinberger ED Schuster P RNA Folding Landscapes and Combinatory Landscapes Phys Rev E 1993 47 2083-2099 10.1103/ PhysRevE.47.2083
26. Yong J Golembe TJ Pellizzoni DJBL Dreyfuss G snRNAs Contain Specific SMN-Binding Domains That Are Essential for snRNP Assembly Mol Cell Biol 2004 24 2747-2756 15024064 10.1128/MCB.24.7.2747-2756.2004 371136
27. Richard P Darzacq X Bertrand E Jády BE Verheggen C Kiss T A common sequence motif determines the Cajal body-specific localization of box H/ACA scaRNAs EMBO J 2003 22 4283-4293 12912925 10.1093/emboj/cdg394 175784
28. Washietl S RNAz http://www.tbi.univie.ac.at/~wash/RNAz/