-
1
-
-
0035656688
-
Non-coding RNA genes and the modern RNA world
-
Eddy SR: Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet. 2001, 2:919-929
-
(2001)
Nat. Rev. Genet.
, vol.2
, pp. 919-929
-
-
Eddy, S.R.1
-
2
-
-
0035171078
-
The non-coding RNAs as riboregulators
-
Erdmann VA, Barciszewska MZ, Symanski M, Hochberg A, de Groot N, Barciszewski J: The non-coding RNAs as riboregulators. Nucl. Acids Res. 2001, 29:189-193
-
(2001)
Nucl. Acids Res.
, vol.29
, pp. 189-193
-
-
Erdmann, V.A.1
Barciszewska, M.Z.2
Symanski, M.3
Hochberg, A.4
de Groot, N.5
Barciszewski, J.6
-
3
-
-
0037133945
-
Computational genomics of noncoding RNA genes
-
Eddy S: Computational genomics of noncoding RNA genes. Cell 2002, 109:137-140
-
(2002)
Cell
, vol.109
, pp. 137-140
-
-
Eddy, S.1
-
4
-
-
0028942159
-
Finding the hairpin in the haystack: Searching for RNA motifs
-
Dandekar T, Hentze MW: Finding the hairpin in the haystack: Searching for RNA motifs. Trends Genet. 1995, 11:45-50
-
(1995)
Trends Genet.
, vol.11
, pp. 45-50
-
-
Dandekar, T.1
Hentze, M.W.2
-
5
-
-
0028258377
-
An RNA pattern matching program with enhanced performance and portability
-
Laferriere A, Gautheret D, Cedergren R: An RNA pattern matching program with enhanced performance and portability. Comput. Applic. Biosci. 1994, 10:211-212
-
(1994)
Comput. Applic. Biosci.
, vol.10
, pp. 211-212
-
-
Laferriere, A.1
Gautheret, D.2
Cedergren, R.3
-
7
-
-
0025864008
-
Identifying potential tRNA genes in genomic DNA sequences
-
Fichant GA, Burks C: Identifying potential tRNA genes in genomic DNA sequences. J. Mol. Biol. 1991, 220:3659-671
-
(1991)
J. Mol. Biol.
, vol.220
, pp. 3659-3671
-
-
Fichant, G.A.1
Burks, C.2
-
8
-
-
0030598363
-
Very fast identification of RNA motifs in genomics DNA. Application to tRNA search in the yeast genome
-
El Mabrouk N, Lisacek F: Very fast identification of RNA motifs in genomics DNA. Application to tRNA search in the yeast genome. J. Mol. Biol. 1996, 46-55
-
(1996)
J. Mol. Biol.
, pp. 46-55
-
-
El Mabrouk, N.1
Lisacek, F.2
-
9
-
-
0030854739
-
tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
Lowe TM, Eddy SR: tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucl. Acids Res. 1997, 25:955-964
-
(1997)
Nucl. Acids Res.
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
10
-
-
0028316745
-
Automatic identification of group I intron cores in genomic DNA sequences
-
Lisacek F, Diaz Y, Michel F: Automatic identification of group I intron cores in genomic DNA sequences. J. Mol. Biol. 1994, 235:1206-1217
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1206-1217
-
-
Lisacek, F.1
Diaz, Y.2
Michel, F.3
-
11
-
-
0030581160
-
Intron-encoded, antisense small nucleolar RNAs: The characterization of nine novel species points to their direct role as guides for the 2′-O-ribose methylation of rRNAs
-
Nicoloso M, Qu LH, Michot B, Bachellerie JP: Intron-encoded, antisense small nucleolar RNAs: The characterization of nine novel species points to their direct role as guides for the 2′-O-ribose methylation of rRNAs. J. Mol. Biol. 1996, 260:178-195
-
(1996)
J. Mol. Biol.
, vol.260
, pp. 178-195
-
-
Nicoloso, M.1
Qu, L.H.2
Michot, B.3
Bachellerie, J.P.4
-
12
-
-
0033582628
-
A computational screen for methylation guide snoRNAs in yeast
-
Lowe TM, Eddy SR: A computational screen for methylation guide snoRNAs in yeast. Science 1998, 283:1168-1171
-
(1998)
Science
, vol.283
, pp. 1168-1171
-
-
Lowe, T.M.1
Eddy, S.R.2
-
13
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucl. Acids Res. 1997, 25:3389-3402
-
(1997)
Nucl. Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
14
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 1988, 85:2444-2448
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
15
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice. Nucl. Acids Res. 1994, 22:4673-4680
-
(1994)
Nucl. Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
16
-
-
0000228203
-
A model of evolutionary change in proteins
-
(Edited by: Dayhoff MO) Washington DC, National Biomedical Research Foundation
-
Dayhoff MO, Schwartz RM, Orcutt BC: A model of evolutionary change in proteins. In: Atlas of Protein Sequence and Structure (Edited by: Dayhoff MO) Washington DC, National Biomedical Research Foundation 1978, 345-352
-
(1978)
Atlas of Protein Sequence and Structure
, pp. 345-352
-
-
Dayhoff, M.O.1
Schwartz, R.M.2
Orcutt, B.C.3
-
17
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 1992, 89:10915-10919
-
(1992)
Proc. Natl. Acad. Sci. USA
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
18
-
-
0028181441
-
Hidden Markov models in computational biology: Applications to protein modeling
-
Krogh A, Brown M, Mian IS, Sjolander K, Haussler D: Hidden Markov models in computational biology: Applications to protein modeling. J. Mol. Biol. 1994, 235:1501-1531
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1501-1531
-
-
Krogh, A.1
Brown, M.2
Mian, I.S.3
Sjolander, K.4
Haussler, D.5
-
19
-
-
0031743421
-
Profile hidden Markov models
-
Eddy SR: Profile hidden Markov models. Bioinformatics 1998, 14:755-763
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
20
-
-
0011542799
-
The Pfam protein families database
-
Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths Jones S, Howe KL, Marshall M, Sonnhammer EL: The Pfam protein families database. Nucl. Acids Res. 2002, 30:276-280
-
(2002)
Nucl. Acids Res.
, vol.30
, pp. 276-280
-
-
Bateman, A.1
Birney, E.2
Cerruti, L.3
Durbin, R.4
Etwiller, L.5
Eddy, S.R.6
Griffiths Jones, S.7
Howe, K.L.8
Marshall, M.9
Sonnhammer, E.L.10
-
21
-
-
0036086410
-
Recent improvements to the SMART domain-based sequence annotation resource
-
Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P: Recent improvements to the SMART domain-based sequence annotation resource. Nucl. Acids Res. 2002, 30:242-244
-
(2002)
Nucl. Acids Res.
, vol.30
, pp. 242-244
-
-
Letunic, I.1
Goodstadt, L.2
Dickens, N.J.3
Doerks, T.4
Schultz, J.5
Mott, R.6
Ciccarelli, F.7
Copley, R.R.8
Ponting, C.P.9
Bork, P.10
-
22
-
-
0028272315
-
RNA sequence analysis using covariance models
-
Eddy SR, Durbin R: RNA sequence analysis using covariance models. Nucl. Acids Res. 1994, 22:2079-2088
-
(1994)
Nucl. Acids Res.
, vol.22
, pp. 2079-2088
-
-
Eddy, S.R.1
Durbin, R.2
-
23
-
-
0028593508
-
Stochastic context-free grammars for tRNA modeling
-
Sakakibara Y, Brown M, Hughey R, Mian IS, Sjolander K, Underwood RC, Haussler D: Stochastic context-free grammars for tRNA modeling. Nucl. Acids Res. 1994, 22:5112-5120
-
(1994)
Nucl. Acids Res.
, vol.22
, pp. 5112-5120
-
-
Sakakibara, Y.1
Brown, M.2
Hughey, R.3
Mian, I.S.4
Sjolander, K.5
Underwood, R.C.6
Haussler, D.7
-
24
-
-
0003516147
-
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
-
Cambridge UK, Cambridge University Press
-
Durbin R, Eddy SR, Krogh A, Mitchison GJ: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge UK, Cambridge University Press 1998
-
(1998)
-
-
Durbin, R.1
Eddy, S.R.2
Krogh, A.3
Mitchison, G.J.4
-
25
-
-
0027982394
-
RNAlign program: Alignment of RNA sequences using both primary and secondary structures
-
Corpet F, Michot B: RNAlign program: Alignment of RNA sequences using both primary and secondary structures. Comput. Applic. Biosci. 1994, 10:389-399
-
(1994)
Comput. Applic. Biosci.
, vol.10
, pp. 389-399
-
-
Corpet, F.1
Michot, B.2
-
28
-
-
0031678285
-
A polyhedral approach to RNA sequence structural alignment
-
Lenhof HP, Reinert K, Vingron M: A polyhedral approach to RNA sequence structural alignment. In: RECOMB 98 ACM Press 1998, 153-162
-
(1998)
RECOMB 98 ACM Press
, pp. 153-162
-
-
Lenhof, H.P.1
Reinert, K.2
Vingron, M.3
-
29
-
-
0031750905
-
A polyhedral approach to RNA sequence structure alignment
-
Lenhof HP, Reinert K, Vingron M: A polyhedral approach to RNA sequence structure alignment. J. Comput. Biol. 1998, 5:517-530
-
(1998)
J. Comput. Biol.
, vol.5
, pp. 517-530
-
-
Lenhof, H.P.1
Reinert, K.2
Vingron, M.3
-
30
-
-
0016518550
-
A linear space algorithm for computing maximal common subsequences
-
Hirschberg DS: A linear space algorithm for computing maximal common subsequences. Communications of the ACM 1975, 18:341-343
-
(1975)
Communications of the ACM
, vol.18
, pp. 341-343
-
-
Hirschberg, D.S.1
-
32
-
-
0025187499
-
Comparing multiple RNA secondary structures using tree comparisons
-
Shapiro BA, Zhang K: Comparing multiple RNA secondary structures using tree comparisons. Comput. Applic. Biosci. 1990, 6:309-318
-
(1990)
Comput. Applic. Biosci.
, vol.6
, pp. 309-318
-
-
Shapiro, B.A.1
Zhang, K.2
-
33
-
-
0022146059
-
Simultaneous solution of the RNA folding, alignment, and protosequence problems
-
Sankoff D: Simultaneous solution of the RNA folding, alignment, and protosequence problems. SIAM J. Appl. Math. 1985, 45:810-825
-
(1985)
SIAM J. Appl. Math.
, vol.45
, pp. 810-825
-
-
Sankoff, D.1
-
34
-
-
0032796501
-
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
-
Knudsen B, Hein J: RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 1999, 15:446-454
-
(1999)
Bioinformatics
, vol.15
, pp. 446-454
-
-
Knudsen, B.1
Hein, J.2
-
35
-
-
0035873307
-
Discovering common stemloop motifs in unaligned RNA sequences
-
Gorodkin J, Stricklin SL, Stormo GD: Discovering common stemloop motifs in unaligned RNA sequences. Nucl. Acids Res. 2001, 29:2135-2144
-
(2001)
Nucl. Acids Res.
, vol.29
, pp. 2135-2144
-
-
Gorodkin, J.1
Stricklin, S.L.2
Stormo, G.D.3
-
36
-
-
0036366014
-
Pairwise RNA structure comparison with stochastic context-free grammars
-
Holmes I, Rubin GM: Pairwise RNA structure comparison with stochastic context-free grammars. Pac. Symp. Biocomput. 2002, 163-174
-
(2002)
Pac. Symp. Biocomput.
, pp. 163-174
-
-
Holmes, I.1
Rubin, G.M.2
-
37
-
-
0036295198
-
Dynalign: An algorithm for finding the secondary structure common to two RNA sequences
-
Mathews DH, Turner DH: Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J. Mol. Biol. 2002, 317:191-203
-
(2002)
J. Mol. Biol.
, vol.317
, pp. 191-203
-
-
Mathews, D.H.1
Turner, D.H.2
-
38
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman SB, Wunsch CD: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 1970, 48:443-453
-
(1970)
J. Mol. Biol.
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
39
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith TF, Waterman MS: Identification of common molecular subsequences. J. Mol. Biol. 1981, 147:195-197
-
(1981)
J. Mol. Biol.
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
40
-
-
0011450901
-
An efficient recognition and syntax algorithm for context-free algorithms
-
Technical Report AFCRL-65-758 Air Force Cambridge Research Lab Bedford, Mass
-
Kasami T: An efficient recognition and syntax algorithm for context-free algorithms. Technical Report AFCRL-65-758 Air Force Cambridge Research Lab Bedford, Mass. 1965
-
(1965)
-
-
Kasami, T.1
-
42
-
-
0003620778
-
Introduction to Automata Theory, Languages, and Computation
-
Addison-Wesley
-
Hopcroft JE, Ullman JD: Introduction to Automata Theory, Languages, and Computation. Addison-Wesley 1979
-
(1979)
-
-
Hopcroft, J.E.1
Ullman, J.D.2
-
43
-
-
0002532056
-
The estimation of stochastic context-free grammars using the INSIDE-OUTSIDE algorithm
-
Lari K, Young SJ: The estimation of stochastic context-free grammars using the INSIDE-OUTSIDE algorithm. Computer Speech and Language 1990, 4:35-56
-
(1990)
Computer Speech and Language
, vol.4
, pp. 35-56
-
-
Lari, K.1
Young, S.J.2
-
44
-
-
0026187099
-
Applications of stochastic context-free grammars using the INSIDE-OUTSIDE algorithm
-
Lari K, Young SJ: Applications of stochastic context-free grammars using the INSIDE-OUTSIDE algorithm. Computer Speech and Language 1991, 5:237-257
-
(1991)
Computer Speech and Language
, vol.5
, pp. 237-257
-
-
Lari, K.1
Young, S.J.2
-
45
-
-
0025832114
-
Inferring consensus structure from nucleic acid sequences
-
Chiu DKY, Kolodziejczak T: Inferring consensus structure from nucleic acid sequences. Comput. Applic. Biosci. 1991, 7:347-352
-
(1991)
Comput. Applic. Biosci.
, vol.7
, pp. 347-352
-
-
Chiu, D.K.Y.1
Kolodziejczak, T.2
-
46
-
-
0026466830
-
Identifying constraints on the higher-order structure of RNA: Continued development and application of comparative sequence analysis methods
-
Gutell RR, Power A, Hertz GZ, Putz EJ, Stormo GD: Identifying constraints on the higher-order structure of RNA: Continued development and application of comparative sequence analysis methods. Nucl. Acids Res. 1992, 20:5785-5795
-
(1992)
Nucl. Acids Res.
, vol.20
, pp. 5785-5795
-
-
Gutell, R.R.1
Power, A.2
Hertz, G.Z.3
Putz, E.J.4
Stormo, G.D.5
-
47
-
-
84937404651
-
Explaining and controlling ambiguity in dynamic programming
-
(Edited by: Giancarlo R, Sankoff D) Montreal, Canada, Springer-Verlag, Berlin
-
Giegerich R: Explaining and controlling ambiguity in dynamic programming. In: Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching (Edited by: Giancarlo R, Sankoff D) Montreal, Canada, Springer-Verlag, Berlin 2000, 1848:46-59
-
(2000)
Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
, vol.1848
, pp. 46-59
-
-
Giegerich, R.1
-
48
-
-
0024610919
-
A tutorial on hidden Markov models and selected applications in speech recognition
-
Rabiner LR: A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE 1989, 77:257-286
-
(1989)
Proc. IEEE
, vol.77
, pp. 257-286
-
-
Rabiner, L.R.1
-
49
-
-
0027244036
-
Compilation of tRNA sequences and sequences of tRNA genes
-
Steinberg S, Misch A, Sprinzl M: Compilation of tRNA sequences and sequences of tRNA genes. Nucl. Acids Res. 1993, 21:3011-3015
-
(1993)
Nucl. Acids Res.
, vol.21
, pp. 3011-3015
-
-
Steinberg, S.1
Misch, A.2
Sprinzl, M.3
-
50
-
-
0036084598
-
5S ribosomal RNA database
-
Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J: 5S ribosomal RNA database. Nucl. Acids Res. 2002, 30:176-178
-
(2002)
Nucl. Acids Res.
, vol.30
, pp. 176-178
-
-
Szymanski, M.1
Barciszewska, M.Z.2
Erdmann, V.A.3
Barciszewski, J.4
-
51
-
-
0025981510
-
SRP-RNA sequence alignment and secondary structure
-
Larsen N, Zwieb C: SRP-RNA sequence alignment and secondary structure. Nucl. Acids Res. 1991, 19:209-215
-
(1991)
Nucl. Acids Res.
, vol.19
, pp. 209-215
-
-
Larsen, N.1
Zwieb, C.2
-
52
-
-
0344298926
-
The ribonuclease P database
-
Brown JW: The ribonuclease P database. Nucl. Acids Res. 1999, 27:314
-
(1999)
Nucl. Acids Res.
, vol.27
, pp. 314
-
-
Brown, J.W.1
-
53
-
-
0027161934
-
Compilation of small ribosomal subunit RNA structures
-
Neefs JM, van Peer de Y, De Rijk P, Chapelle S, De Wachter R: Compilation of small ribosomal subunit RNA structures. Nucl. Acids Res. 1993, 21:3025-3049
-
(1993)
Nucl. Acids Res.
, vol.21
, pp. 3025-3049
-
-
Neefs, J.M.1
van Peer de, Y.2
De Rijk, P.3
Chapelle, S.4
De Wachter, R.5
-
54
-
-
0028060568
-
Database on the structure of large ribosomal subunit RNA
-
De Rijk P, Van Peer de Y, Chapelle S, De Wachter R: Database on the structure of large ribosomal subunit RNA. Nucl. Acids Res. 1994, 22:3495-3501
-
(1994)
Nucl. Acids Res.
, vol.22
, pp. 3495-3501
-
-
De Rijk, P.1
Van Peer de, Y.2
Chapelle, S.3
De Wachter, R.4
-
55
-
-
0033524952
-
A dynamic programming algorithm for RNA structure prediction including pseudoknots
-
Rivas E, Eddy SR: A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol. 1999, 285:2053-2068
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 2053-2068
-
-
Rivas, E.1
Eddy, S.R.2
-
56
-
-
0034046133
-
The language of RNA: A formal grammar that includes pseudoknots
-
Rivas E, Eddy SR: The language of RNA: A formal grammar that includes pseudoknots. Bioinformatics 2000, 16:326-333
-
(2000)
Bioinformatics
, vol.16
, pp. 326-333
-
-
Rivas, E.1
Eddy, S.R.2
-
57
-
-
0029906607
-
Dirichlet mixtures: A method for improving detection of weak but significant protein sequence homology
-
Sjolander K, Karplus K, Brown M, Hughey R, Krogh A, Mian IS, Haussler D: Dirichlet mixtures: A method for improving detection of weak but significant protein sequence homology. Comput. Applic. Biosci. 1996, 12:327-345
-
(1996)
Comput. Applic. Biosci.
, vol.12
, pp. 327-345
-
-
Sjolander, K.1
Karplus, K.2
Brown, M.3
Hughey, R.4
Krogh, A.5
Mian, I.S.6
Haussler, D.7
|