-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
-
(1990)
J. Mol. Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
2
-
-
0021910176
-
Transcription and excision of a large intron in the tRNATrp gene of an archaebacterium
-
Daniels, C.J., Gupta, R., and Doolittle, W.F. 1985. Transcription and excision of a large intron in the tRNATrp gene of an archaebacterium, Halobacterium volcanii. J. Biol. Chem. 260: 3132-3134.
-
(1985)
Halobacterium volcanii. J. Biol. Chem
, vol.260
, pp. 3132-3134
-
-
Daniels, C.J.1
Gupta, R.2
Doolittle, W.F.3
-
3
-
-
0024547073
-
Presence of an intron in elongator methionine-tRNA of Halobacterium volcanii
-
Datta, P.K., Hawkins, L.K., and Gupta, R. 1989. Presence of an intron in elongator methionine-tRNA of Halobacterium volcanii. Can. J. Microbiol. 35: 189-194.
-
(1989)
Can. J. Microbiol
, vol.35
, pp. 189-194
-
-
Datta, P.K.1
Hawkins, L.K.2
Gupta, R.3
-
4
-
-
0028272315
-
RNA sequence analysis using covariance models
-
Eddy, S.R. and Durbin, R. 1994. RNA sequence analysis using covariance models. Nucleic Acids Res. 22: 2079-2088.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 2079-2088
-
-
Eddy, S.R.1
Durbin, R.2
-
5
-
-
0025864008
-
Identifying potential tRNA genes in genomic DNA sequences
-
Fichant, G.A. and Burks, C. 1991. Identifying potential tRNA genes in genomic DNA sequences. J. Mol. Biol. 220: 659-671.
-
(1991)
J. Mol. Biol
, vol.220
, pp. 659-671
-
-
Fichant, G.A.1
Burks, C.2
-
6
-
-
0037154277
-
Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum
-
Fitz-Gibbon, S.T., Ladner, H., Kim, U.J., Stetter, K.O., Simon, M.I., and Miller, J.H. 2002. Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc. Natl. Acad. Sci. 99: 984-989.
-
(2002)
Proc. Natl. Acad. Sci
, vol.99
, pp. 984-989
-
-
Fitz-Gibbon, S.T.1
Ladner, H.2
Kim, U.J.3
Stetter, K.O.4
Simon, M.I.5
Miller, J.H.6
-
7
-
-
33845286513
-
Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum
-
Hallam, S.J., Konstantinidis, K.T., Putnam, N., Schleper, C., Watanabe, Y., Sugahara, J., Preston, C., de la Torre, J., Richardson, P.M., and Delong, E.F. 2006. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc. Natl. Acad. Sci. 103: 18296-18301.
-
(2006)
Proc. Natl. Acad. Sci
, vol.103
, pp. 18296-18301
-
-
Hallam, S.J.1
Konstantinidis, K.T.2
Putnam, N.3
Schleper, C.4
Watanabe, Y.5
Sugahara, J.6
Preston, C.7
de la Torre, J.8
Richardson, P.M.9
Delong, E.F.10
-
8
-
-
0020772838
-
Putative introns in tRNA genes of prokaryotes
-
Kaine, B.P., Gupta, R., and Woese, C.R. 1983. Putative introns in tRNA genes of prokaryotes. Proc. Natl. Acad. Sci. 80: 3309-3312.
-
(1983)
Proc. Natl. Acad. Sci
, vol.80
, pp. 3309-3312
-
-
Kaine, B.P.1
Gupta, R.2
Woese, C.R.3
-
9
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
Katoh, K., Kuma, K., Toh, H., and Miyata, T. 2005. MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33: 511-518.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
10
-
-
0024978663
-
A unique tRNA intron in the variable loop of the extreme thermophile Thermofilum pendens and its possible evolutionary implications
-
Kjems, J., Leffers, H., Olesen, T., and Garrett, R.A. 1989. A unique tRNA intron in the variable loop of the extreme thermophile Thermofilum pendens and its possible evolutionary implications. J. Biol. Chem. 264: 17834-17837.
-
(1989)
J. Biol. Chem
, vol.264
, pp. 17834-17837
-
-
Kjems, J.1
Leffers, H.2
Olesen, T.3
Garrett, R.A.4
-
11
-
-
0030730242
-
Properties of H. volcanii tRNA intron endonuclease reveal a relationship between the archaeal and eucaryal tRNA intron processing systems
-
Kleman-Leyer, K., Armbruster, D.W., and Daniels, C.J. 1997. Properties of H. volcanii tRNA intron endonuclease reveal a relationship between the archaeal and eucaryal tRNA intron processing systems. Cell 89: 839-847.
-
(1997)
Cell
, vol.89
, pp. 839-847
-
-
Kleman-Leyer, K.1
Armbruster, D.W.2
Daniels, C.J.3
-
12
-
-
0030854739
-
tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
Lowe, T.M. and Eddy, S.R. 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
13
-
-
0344874260
-
Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: Evolutionary implications
-
Marck, C. and Grosjean, H. 2003. Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: Evolutionary implications. RNA 9: 1516-1531.
-
(2003)
RNA
, vol.9
, pp. 1516-1531
-
-
Marck, C.1
Grosjean, H.2
-
14
-
-
27944453600
-
Virtual Footprint and PRODORIC: An integrative framework for regulon prediction in prokaryotes
-
Munch, R., Hiller, K., Grote, A., Scheer, M., Klein, J., Schobert, M., and Jahn, D. 2005. Virtual Footprint and PRODORIC: An integrative framework for regulon prediction in prokaryotes. Bioinformatics 21: 4187-4189.
-
(2005)
Bioinformatics
, vol.21
, pp. 4187-4189
-
-
Munch, R.1
Hiller, K.2
Grote, A.3
Scheer, M.4
Klein, J.5
Schobert, M.6
Jahn, D.7
-
15
-
-
0028214356
-
Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of transcriptional control regions
-
Pavesi, A., Conterio, F., Bolchi, A., Dieci, G., and Ottonello, S. 1994. Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of transcriptional control regions. Nucleic Acids Res. 22: 1247-1256.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 1247-1256
-
-
Pavesi, A.1
Conterio, F.2
Bolchi, A.3
Dieci, G.4
Ottonello, S.5
-
16
-
-
19444384556
-
The complete set of tRNA species in Nanoarchaeum equitans
-
Randau, L., Pearson, M., and Soll, D. 2005. The complete set of tRNA species in Nanoarchaeum equitans. FEBS Lett. 579: 2945-2947.
-
(2005)
FEBS Lett
, vol.579
, pp. 2945-2947
-
-
Randau, L.1
Pearson, M.2
Soll, D.3
-
17
-
-
0028196714
-
From sequences to shapes and back: A case study in RNA secondary structures
-
Schuster, P., Fontana, W., Stadler, P.F., and Hofacker, I.L. 1994. From sequences to shapes and back: A case study in RNA secondary structures. Proc. Biol. Sci. 255: 279-284.
-
(1994)
Proc. Biol. Sci
, vol.255
, pp. 279-284
-
-
Schuster, P.1
Fontana, W.2
Stadler, P.F.3
Hofacker, I.L.4
-
18
-
-
0034945083
-
The complete genome of the crenarchaeon Sulfolobus solfataricus P2
-
She, Q., Singh, R.K., Confalonieri, F., Zivanovic, Y., Allard, G., Awayez, M.J., Chan-Weiher, C.C., Clausen, I.G., Curtis, B.A., De Moors, A., et al. 2001. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc. Natl. Acad. Sci. 98: 7835-7840.
-
(2001)
Proc. Natl. Acad. Sci
, vol.98
, pp. 7835-7840
-
-
She, Q.1
Singh, R.K.2
Confalonieri, F.3
Zivanovic, Y.4
Allard, G.5
Awayez, M.J.6
Chan-Weiher, C.C.7
Clausen, I.G.8
Curtis, B.A.9
De Moors, A.10
-
19
-
-
0037007150
-
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens
-
Slesarev, A.I., Mezhevaya, K.V., Makarova, K.S., Polushin, N.N., Shcherbinina, O.V., Shakhova, V.V., Belova, G.I., Aravind, L., Natale, D.A., Rogozin, I.B., et al. 2002. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc. Natl. Acad. Sci. 99: 4644-4649.
-
(2002)
Proc. Natl. Acad. Sci
, vol.99
, pp. 4644-4649
-
-
Slesarev, A.I.1
Mezhevaya, K.V.2
Makarova, K.S.3
Polushin, N.N.4
Shcherbinina, O.V.5
Shakhova, V.V.6
Belova, G.I.7
Aravind, L.8
Natale, D.A.9
Rogozin, I.B.10
-
20
-
-
15644383855
-
Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: Functional analysis and comparative genomics
-
Smith, D.R., Doucette-Stamm, L.A., Deloughery, C., Lee, H., Dubois, J., Aldredge, T., Bashirzadeh, R., Blakely, D., Cook, R., Gilbert, K., et al. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: Functional analysis and comparative genomics. J. Bacteriol. 179: 7135-7155.
-
(1997)
J. Bacteriol
, vol.179
, pp. 7135-7155
-
-
Smith, D.R.1
Doucette-Stamm, L.A.2
Deloughery, C.3
Lee, H.4
Dubois, J.5
Aldredge, T.6
Bashirzadeh, R.7
Blakely, D.8
Cook, R.9
Gilbert, K.10
-
21
-
-
33845244847
-
SPLITS: A new program for predicting split and intron-containing tRNA genes at the genome level
-
Sugahara, J., Yachie, N., Sekine, Y., Soma, A., Matsui, M., Tomita, M., and Kanai, A. 2006. SPLITS: A new program for predicting split and intron-containing tRNA genes at the genome level. In Silico Biol. 6: 411-418.
-
(2006)
In Silico Biol
, vol.6
, pp. 411-418
-
-
Sugahara, J.1
Yachie, N.2
Sekine, Y.3
Soma, A.4
Matsui, M.5
Tomita, M.6
Kanai, A.7
-
22
-
-
0037082426
-
RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing
-
Tang, T.H., Rozhdestvensky, T.S., d'Orval, B.C., Bortolin, M.L., Huber, H., Charpentier, B., Branlant, C., Bachellerie, J.P., Brosius, J., and Huttenhofer, A. 2002. RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing. Nucleic Acids Res. 30: 921-930.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 921-930
-
-
Tang, T.H.1
Rozhdestvensky, T.S.2
d'Orval, B.C.3
Bortolin, M.L.4
Huber, H.5
Charpentier, B.6
Branlant, C.7
Bachellerie, J.P.8
Brosius, J.9
Huttenhofer, A.10
-
23
-
-
0024547780
-
Transfer RNA intron processing in the halophilic archaebacteria
-
Thompson, L.D., Brandon, L.D., Nieuwlandt, D.T., and Daniels, C.J. 1989. Transfer RNA intron processing in the halophilic archaebacteria. Can. J. Microbiol. 35: 36-42.
-
(1989)
Can. J. Microbiol
, vol.35
, pp. 36-42
-
-
Thompson, L.D.1
Brandon, L.D.2
Nieuwlandt, D.T.3
Daniels, C.J.4
-
24
-
-
21144453167
-
Structure, function, and evolution of the tRNA endonucleases of Archaea: An example of subfunctionalization
-
Tocchini-Valentini, G.D., Fruscoloni, P., and Tocchini-Valentini, G.P. 2005. Structure, function, and evolution of the tRNA endonucleases of Archaea: An example of subfunctionalization. Proc. Natl. Acad. Sci. 102: 8933-8938.
-
(2005)
Proc. Natl. Acad. Sci
, vol.102
, pp. 8933-8938
-
-
Tocchini-Valentini, G.D.1
Fruscoloni, P.2
Tocchini-Valentini, G.P.3
-
25
-
-
0017883374
-
Structure of yeast phenylalanine-tRNA genes: An intervening DNA segment within the region coding for the tRNA
-
Valenzuela, P., Venegas, A., Weinberg, F., Bishop, R., and Rutter, W.J. 1978. Structure of yeast phenylalanine-tRNA genes: An intervening DNA segment within the region coding for the tRNA. Proc. Natl. Acad. Sci. 75: 190-194.
-
(1978)
Proc. Natl. Acad. Sci
, vol.75
, pp. 190-194
-
-
Valenzuela, P.1
Venegas, A.2
Weinberg, F.3
Bishop, R.4
Rutter, W.J.5
-
26
-
-
0037005991
-
Introns in protein-coding genes in Archaea
-
Watanabe, Y., Yokobori, S., Inaba, T., Yamagishi, A., Oshima, T., Kawarabayasi, Y., Kikuchi, H., and Kita, K. 2002. Introns in protein-coding genes in Archaea. FEBS Lett. 510: 27-30.
-
(2002)
FEBS Lett
, vol.510
, pp. 27-30
-
-
Watanabe, Y.1
Yokobori, S.2
Inaba, T.3
Yamagishi, A.4
Oshima, T.5
Kawarabayasi, Y.6
Kikuchi, H.7
Kita, K.8
-
27
-
-
0001580909
-
Genes for stable RNA in the extreme thermophile Thermoproteus tenax: Introns and transcription signals
-
Wich, G., Leinfelder, W., and Bock, A. 1987. Genes for stable RNA in the extreme thermophile Thermoproteus tenax: Introns and transcription signals. EMBO J. 6: 523-528.
-
(1987)
EMBO J
, vol.6
, pp. 523-528
-
-
Wich, G.1
Leinfelder, W.2
Bock, A.3
-
28
-
-
33745206275
-
Archaeal pre-mRNA splicing: A connection to hetero-oligomeric splicing endonuclease
-
Yoshinari, S., Itoh, T., Hallam, S.J., DeLong, E.F., Yokobori, S., Yamagishi, A., Oshima, T., Kita, K., and Watanabe, Y. 2006. Archaeal pre-mRNA splicing: A connection to hetero-oligomeric splicing endonuclease. Biochem. Biophys. Res. Commun. 346: 1024-1032.
-
(2006)
Biochem. Biophys. Res. Commun
, vol.346
, pp. 1024-1032
-
-
Yoshinari, S.1
Itoh, T.2
Hallam, S.J.3
DeLong, E.F.4
Yokobori, S.5
Yamagishi, A.6
Oshima, T.7
Kita, K.8
Watanabe, Y.9
|