-
1
-
-
35549004515
-
Semiautomated improvement of RNA alignments
-
DOI 10.1261/rna.215407
-
Andersen, E.S., Lind-Thomsen, A., Knudsen, B., Kristensen, S.E., Havgaard, J.H., Torarinsson, E., Larsen, N., Zwieb, C., Sestoft, P., Kjems, J. and Gorodkin, J. (2007) Semiautomated Improvement of RNA Alignments, Rna-a Publication of the RNA Society, Vol. 13, pp.1850-1859. (Pubitemid 350005210)
-
(2007)
RNA
, vol.13
, Issue.11
, pp. 1850-1859
-
-
Andersen, E.S.1
Lind-Thomsen, A.2
Knudsen, B.3
Kristensen, S.E.4
Havgaard, J.H.5
Torarinsson, E.6
Larsen, N.7
Zwieb, C.8
Sestoft, P.9
Kjems, J.10
Gorodkin, J.11
-
2
-
-
39149120310
-
Colorstock, SScolor, Raton: RNA alignment visualization tools
-
DOI 10.1093/bioinformatics/btm635
-
Bendaña, Y.R. and Holmes, I.H. (2008) 'Colorstock, SScolor, Raton: RNA alignment visualization tools', Bioinformatics, Vol. 24, pp.579-580. (Pubitemid 351256304)
-
(2008)
Bioinformatics
, vol.24
, Issue.4
, pp. 579-580
-
-
Bendana, Y.R.1
Holmes, I.H.2
-
3
-
-
0344298926
-
The ribonuclease P database
-
DOI 10.1093/nar/27.1.314
-
Brown, J.W. (1999) 'The ribonuclease P database', Nucleic Acids Research, Vol. 27, p.314. (Pubitemid 29209471)
-
(1999)
Nucleic Acids Research
, vol.27
, Issue.1
, pp. 314
-
-
Brown, J.W.1
-
4
-
-
0025900071
-
Phylogenetic analysis and evolution of RNase P RNA in proteobacteria
-
Brown, J.W., Haas, E.S., James, B., Hunt, D.A., Liu, J. and Pace, N.R. (1991) 'Phylogenetic analysis and evolution of RNase P RNA in proteobacteria', Journal of Bacteriology, Vol. 173, pp.3855-3863.
-
(1991)
Journal of Bacteriology
, vol.173
, pp. 3855-3863
-
-
Brown, J.W.1
Haas, E.S.2
James, B.3
Hunt, D.A.4
Liu, J.5
Pace, N.R.6
-
5
-
-
1342288004
-
The jalview java alignment editor
-
Clamp, M., Cuff, J., Searle, S.M. and Barton, G.J. (2004) 'The jalview java alignment editor', Bioinformatics, Vol. 20, pp.426, 427.
-
(2004)
Bioinformatics
, vol.20
, Issue.427
, pp. 426
-
-
Clamp, M.1
Cuff, J.2
Searle, S.M.3
Barton, G.J.4
-
6
-
-
0034894278
-
PAL: An object-oriented programming library for molecular evolution and phylogenetics
-
Drummond, A. and Strimmer, K. (2001) 'PAL: an object-oriented programming library for molecular evolution and phylogenetics', Bioinformatics, Vol. 17, pp.662, 663.
-
(2001)
Bioinformatics
, vol.17
, Issue.663
, pp. 662
-
-
Drummond, A.1
Strimmer, K.2
-
7
-
-
0028272315
-
RNA sequence analysis using covariance models
-
Eddy, S.R. and Durbin, R. (1994) 'RNA sequence analysis using covariance models', Nucleic Acids Res., Vol. 22, pp.2079-2088. (Pubitemid 24192908)
-
(1994)
Nucleic Acids Research
, vol.22
, Issue.11
, pp. 2079-2088
-
-
Eddy, S.R.1
Durbin, R.2
-
8
-
-
84959747425
-
Toward defining the course of evolution: Minimum change for a specified tree topology
-
Fitch, W.M. (1971) 'Toward defining the course of evolution: minimum change for a specified tree topology', Systematic Zoology, Vol. 20, pp.406-416.
-
(1971)
Systematic Zoology
, vol.20
, pp. 406-416
-
-
Fitch, W.M.1
-
9
-
-
58149191274
-
Rfam: Updates to the RNA families database
-
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. and Bateman, A. (2009) 'Rfam: updates to the RNA families database', Nucleic Acids Research, Vol. 37, pp.D136-D140.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Gardner, P.P.1
Daub, J.2
Tate, J.G.3
Nawrocki, E.P.4
Kolbe, D.L.5
Lindgreen, S.6
Wilkinson, A.C.7
Finn, R.D.8
Griffiths-Jones, S.9
Eddy, S.R.10
Bateman, A.11
-
10
-
-
13444309635
-
RALEE-RNA alignment editor in emacs
-
Griffiths-Jones, S. (2005) 'RALEE-RNA alignment editor in emacs', Bioinformatics, Vol. 21, pp.257-259.
-
(2005)
Bioinformatics
, vol.21
, pp. 257-259
-
-
Griffiths-Jones, S.1
-
11
-
-
0037252684
-
Rfam: An RNA family database
-
DOI 10.1093/nar/gkg006
-
Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A. and Eddy, S.R. (2003) 'Rfam: an RNA family database', Nucleic Acids Research, Vol. 31, pp.439-441. (Pubitemid 36150423)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 439-441
-
-
Griffiths-Jones, S.1
Bateman, A.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
-
12
-
-
0028261409
-
Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective
-
Gutell, R.R., Larsen, N. and Woese, C.R. (1994) 'Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective', Microbiology Reviews, Vol. 58, pp.10-26.
-
(1994)
Microbiology Reviews
, vol.58
, pp. 10-26
-
-
Gutell, R.R.1
Larsen, N.2
Woese, C.R.3
-
13
-
-
53749085245
-
Fast and accurate search for non-coding RNA pseudoknot structures in genomes
-
Huang, Z., Wu, Y., Robertson, J., Feng, L., Malmberg, R.L. and Cai, L. (2008) 'Fast and accurate search for non-coding RNA pseudoknot structures in genomes', Bioinformatics, Vol. 24, pp.2281-2287.
-
(2008)
Bioinformatics
, vol.24
, pp. 2281-2287
-
-
Huang, Z.1
Wu, Y.2
Robertson, J.3
Feng, L.4
Malmberg, R.L.5
Cai, L.6
-
14
-
-
25144458057
-
Sequence to Structure (S2S): Display, manipulate and interconnect RNA data from sequence to structure
-
DOI 10.1093/bioinformatics/bti504
-
Jossinet, F. and Westhof, E. (2005) 'Sequence to structure (S2S): display, manipulate and interconnect RNA data from sequence to structure', Bioinformatics, Vol. 21, pp.3320-3321. (Pubitemid 41418451)
-
(2005)
Bioinformatics
, vol.21
, Issue.15
, pp. 3320-3321
-
-
Jossinet, F.1
Westhof, E.2
-
15
-
-
6944242754
-
A universal telomerase RNA core structure includes structured motifs required for binding the telomerase reverse transcriptase protein
-
DOI 10.1073/pnas.0405879101
-
Lin, J., Ly, H., Hussain, A., Abraham, M., Pearl, S., Tzfati, Y., Parslow, T.G. and Blackburn, E.H. (2004) 'A universal telomerase RNA core structure includes structured motifs required for binding the telomerase reverse transcriptase protein', Proc. Natl. Acad. Sci. USA, Vol. 101, pp.14713-14718. (Pubitemid 39410740)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.41
, pp. 14713-14718
-
-
Lin, J.1
Ly, H.2
Hussain, A.3
Abraham, M.4
Pearl, S.5
Tzfati, Y.6
Parslow, T.G.7
Blackburn, E.H.8
-
16
-
-
34250899706
-
Efficient annotation of non-coding RNA structures including pseudoknots via automated filters
-
Liu, C., Song, Y., Hu, P., Malmberg, R.L. and Cai, L. (2006) 'Efficient annotation of non-coding RNA structures including pseudoknots via automated filters', Comput. Syst. Bioinformatics Conf., Stanford, CA, USA, pp.99-110.
-
(2006)
Comput. Syst. Bioinformatics Conf., Stanford, CA, USA
, pp. 99-110
-
-
Liu, C.1
Song, Y.2
Hu, P.3
Malmberg, R.L.4
Cai, L.5
-
18
-
-
71849109186
-
The tedious task of finding homologous noncoding RNA genes
-
Menzel, P., Gorodkin, J. and Stadler, P.F. (2009) 'The tedious task of finding homologous noncoding RNA genes', RNA, Vol. 15, pp.2075-2082.
-
(2009)
RNA
, vol.15
, pp. 2075-2082
-
-
Menzel, P.1
Gorodkin, J.2
Stadler, P.F.3
-
20
-
-
33646272409
-
Identification and classification of conserved RNA secondary structures in the human genome
-
Pedersen, J.S., Bejerano, G., Siepel, A., Rosenbloom, K., Lindblad-Toh, K., Lander, E.S., Kent, J., Miller, W. and Haussler, D. (2006) 'Identification and classification of conserved RNA secondary structures in the human genome', Plos Computational Biology, Vol. 2, pp.251-262.
-
(2006)
Plos Computational Biology
, vol.2
, pp. 251-262
-
-
Pedersen, J.S.1
Bejerano, G.2
Siepel, A.3
Rosenbloom, K.4
Lindblad-Toh, K.5
Lander, E.S.6
Kent, J.7
Miller, W.8
Haussler, D.9
-
21
-
-
40449086374
-
From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal
-
DOI 10.1261/rna.881308
-
Smit, S., Rother, K., Heringa, J. and Knight, R. (2008) 'From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal', RNA, Vol. 14, pp.410-416. (Pubitemid 351397805)
-
(2008)
RNA
, vol.14
, Issue.3
, pp. 410-416
-
-
Smit, S.1
Rother, K.2
Heringa, J.3
Knight, R.4
-
22
-
-
33745492418
-
Tree decomposition based fast search of RNA structures including pseudoknots in genomes
-
1498024, Proceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005
-
Song, Y., Liu, C., Malmberg, R., Pan, F. and Cai, L. (2005) 'Tree decomposition based fast search of RNA structures including pseudoknots in genomes', Proc. IEEE Comput. Syst. Bioinform. Conf., Stanford, CA, USA, pp.223-234. (Pubitemid 43959590)
-
(2005)
Proceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005
, vol.2005
, pp. 223-234
-
-
Song, Y.1
Malmberg, R.2
Liu, C.3
Pan, F.4
Cai, L.5
-
23
-
-
65449188232
-
Jalview version 2 - A multiple sequence alignment editor and analysis workbench
-
doi:10.1093/bioinformatics/btp033
-
Waterhouse, A.M., Procter, J.B., Martin, D.M.A., Clamp, M. and Barton, G.J. (2009) 'Jalview version 2 - a multiple sequence alignment editor and analysis workbench', Bioinformatics, Vol. 25, pp.1189-1191, doi:10.1093/ bioinformatics/btp033.
-
(2009)
Bioinformatics
, vol.25
, pp. 1189-1191
-
-
Waterhouse, A.M.1
Procter, J.B.2
Martin, D.M.A.3
Clamp, M.4
Barton, G.J.5
-
24
-
-
0029907105
-
Phylogenetic analysis of tmRNA secondary structure
-
Williams, K.P. and Bartel, D.P. (1996) 'Phylogenetic analysis of tmRNA secondary structure', RNA, Vol. 2, pp.1306-1310. (Pubitemid 26419224)
-
(1996)
RNA
, vol.2
, Issue.12
, pp. 1306-1310
-
-
Williams, K.P.1
Bartel, D.P.2
-
25
-
-
0033040345
-
Minimal-risk scoring matrices for sequence analysis
-
Wu, T.D., Nevill-Manning, C.G. and Brutlag, D.L. (1999) 'Minimal-risk scoring matrices for sequence analysis', Computational Biology, Vol. 6, pp.219-235. (Pubitemid 29321434)
-
(1999)
Journal of Computational Biology
, vol.6
, Issue.2
, pp. 219-235
-
-
Wu, T.D.1
Nevill-Manning, C.G.2
Brutlag, D.L.3
-
26
-
-
33749516630
-
Principles of micro-RNA production and maturation
-
DOI 10.1038/sj.onc.1209908, PII 1209908
-
Zeng, Y. (2006) 'Principles of micro-RNA production and maturation', Oncogene, Vol. 25, pp.6156-6162. (Pubitemid 44527845)
-
(2006)
Oncogene
, vol.25
, Issue.46
, pp. 6156-6162
-
-
Zeng, Y.1
-
27
-
-
0037246703
-
TmRDB (tmRNA database)
-
Zwieb, C., Gorodkin, J., Knudsen, B., Burks, J. and Wower, J. (2003) 'tmRDB (tmRNA database)', Nucleic Acids Research, Vol. 31, pp.446, 447.
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.447
, pp. 446
-
-
Zwieb, C.1
Gorodkin, J.2
Knudsen, B.3
Burks, J.4
Wower, J.5
|