Nucleic Acids Research, 2003, Vol. 31, No. 1 439-441
© 2003 Oxford University Press
Rfam: an RNA family database
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK 1 Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
*To whom correspondence should be addressed. Tel: +44 1223 834244; Fax: +44 1223 494919; Email: sgj{at}sanger.ac.uk
Received August 15, 2002; Accepted September 1, 2002
ABSTRACT
Rfam is a collection of multiple sequence alignments and covariance models representing non-coding RNA families. Rfam is available on the web in the UK at http://www.sanger.ac.uk/Software/Rfam/ and in the US at http://rfam.wustl.edu/. These websites allow the user to search a query sequence against a library of covariance models, and view multiple sequence alignments and family annotation. The database can also be downloaded in flatfile form and searched locally using the INFERNAL package (http://infernal.wustl.edu/). The first release of Rfam (1.0) contains 25 families, which annotate over 50 000 non-coding RNA genes in the taxonomic divisions of the EMBL nucleotide database.
INTRODUCTION
Non-coding RNA genes produce a functional RNA molecule as a final product, rather than a translated protein. Current gene-finding methods largely ignore non-coding RNA genes, yet they produce some of the cell's most important products—transfer RNA and ribosomal RNA are two of the well-known examples. The number of known RNA genes is expanding rapidly due to the deluge of genomic data, but also aided by recent systematic efforts to detect RNA genes [reviewed in (1–3)].
Just like protein coding genes ncRNAs fall into families that have evolved from a common ancestor. By making alignments of these families of ncRNA genes we can learn about their structure and function. Indeed, accurate prediction of RNA secondary structure relies on multiple sequence alignments to provide data on co-varying bases (4). Ribosomal RNA alignments are used to make molecular phylogenies that guide taxonomic classification of all species (5).
Many RNA sequence families conserve a consensus base-paired secondary structure. Standard primary sequence analysis tools [such as BLAST (6) for database searches and CLUSTALW (7) for multiple alignment] are useful for closely related RNAs, but recognition and alignment of more distantly related structural RNAs is greatly aided by consensus secondary structure information. Historically, structure-based RNA sequence analysis has been difficult to automate. Most RNA structural alignments are the product of expert manual curation. Recent software advances (8) using secondary structure profiles called ‘covariance models’ (CMs—also called profile stochastic context-free grammars) (1,9) have led us to begin the development and automated maintenance of a database of structural RNA alignments. This is analogous to the use of profile hidden Markov models of primary sequence consensus in the development and maintenance of thousands of protein sequence alignments in the Pfam database (10).
Several databases already exist that contain RNA alignments and information—for example, the European Large Subunit Ribosomal RNA Database (11), the SRP database (12), the uRNA database (13), the Comparative RNA Web (14), and others (15–22). These databases are well curated and provide a large amount of information to the specialist. However, they vary greatly in the file formats used and the data presented. There are also several specialised computational tools to aid identification of specific RNA types. For example, tRNAscan-SE is a standard tool in the genome annotation field for identifying tRNA genes with extremely high sensitivity and specificity (23). A recent report describes a new tool, BRUCE, which aims to predict tmRNA genes in genomic sequence (24). However, the RNA analysis field lacks any analogue to the comprehensive secondary sequence databases that greatly aid protein annotation, such as Pfam (10), SMART (25) and Prosite (26).
The aims of the Rfam database are (i) to integrate the many existing curated structural RNA alignments (in addition to new alignments) into a common structure-annotated format, analogous to Pfam's curated seed alignments; (ii) to use covariance model software to search the growing sequence databases and maintain automatically-generated alignments of all detectable homologues, analogous to Pfam's automatically-generated full alignments; and (iii) to provide a system for automatically analysing and annotating sequences (including complete genome sequences) for the presence of homologues to known structural RNAs, analogous to the public Pfam search servers.
METHODS
Each family in Rfam is represented by two multiple sequence alignments and a covariance model. The seed alignment contains known representative members of the family, is hand-curated, and is annotated with structural information. The seed alignment is used to build a covariance model using the CMBUILD program from the INFERNAL suite (http://infernal.wustl.edu/) (8). The model is then used to search a nucleotide sequence database using the CMSEARCH program. CMSEARCH reports scores for matches to the model, and a family-specific threshold is chosen such that we believe no false positives fall above the threshold. The matches are then aligned to the model using the CMALIGN program.
The nucleotide database searched is called RFAMSEQ, and is built from a subset of the EMBL nucleotide database (27). RFAMSEQ 1 is based on EMBL release 71. RFAMSEQ includes the ‘finished’ portion of EMBL distributed in the organism specific data files, and excludes the EST, GSS, HTG, HTC, STS and patent sections of the database. Despite these exclusions, RFAMSEQ 1 contains 1 075 317 sequences and over 5.3 billion bases. CM searches are particularly computationally expensive, with a small model (such as tRNA) searching around 200 bases per second on a 600 MHz Compaq ALPHA. A full CM search of RFAMSEQ with one small model would take around 300 cpu days. The search time scales roughly with the cube of the query consensus length, so this quickly becomes entirely infeasible for larger RNAs. We, therefore, employ an initial BLAST search (6) with relaxed search parameters to reduce the search space. All BLAST hits with P-value <10 to a member of the seed alignment are retrieved, a family specific window size added to each end of the matches, and the reduced database subjected to a full CM search. This approach is similar to that employed by the tRNAscan-SE program which uses an heuristic first step followed by full covariance model search (23), but is generally applicable to any ncRNA search. We anticipate that technological and software improvements will in the future allow us to conduct full CM searches to build family alignments.
AVAILABILITY
Rfam is available on the web at http://www.sanger.ac.uk/Software/Rfam/ in the UK, and http://rfam.wustl.edu/ in the US. The database is also available in flatfile format for local installation. To search Rfam locally, the user will also need the INFERNAL software suite, available from http://infernal.wustl.edu/. Table 1 shows a list of families contained in Rfam 1.0. These families annotate over 50 000 ncRNAs in the RFAMSEQ database.
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WEBSITE FEATURES
The Rfam websites have been designed to be intuitive to use—users of the Pfam database of protein families will recognise the layout and format of the database. The websites provide the facility to search a DNA sequence against the library of CMs. The user can view annotation on each RNA family, and follow links to other databases and literature references. The multiple sequence alignments on which Rfam is based are available in a number of formats for viewing in a browser or for downloading. Both the seed and full alignments contain secondary structure mark-up to describe the base-paired positions in the member sequences, and the web view provides a colour-encoded representation of these co-varying columns (Fig. 1). In addition the web pages allow the user to quickly determine the species distribution within a family.
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FUTURE DIRECTIONS
Rfam is under active development and will increase significantly in size and scope over the next 12 months. Novel ncRNA genes are being discovered at a rapid rate, and we aim to quickly translate such discoveries into useful and searchable RNA families. However, we recognise a number of limitations with our approach. The most obvious of these is the computational cost of using CMs. We predict that technological advances will soon make these searches far more feasible, and will allow full CM genome-wide searches for ncRNAs using Rfam. Until such a time narrowing the search space using BLAST greatly facilitates such searches, though at an inevitable and unknown cost in search sensitivity. In addition, there are RNA families that we cannot model using the alignment- and profile-based approach at present—for example, microRNAs (miRNA precursor secondary structures are only vaguely similar stem-loops) and many small nucleolar RNAs (the consensus of modification guide snoRNAs includes significant inter-molecular base pairing to their target RNAs). Despite such limitations, the Rfam library of alignments and CMs provides a useful tool for genome annotation, as well as a comprehensive resource for RNA family information and multiple sequence alignments.
ACKNOWLEDGEMENTS
We are grateful to William Mifsud for providing annotation for many of the families in Rfam.
REFERENCES
- Eddy,S.R. (2002) Computational genomics of noncoding RNA genes. Cell, 109, 137–140.[CrossRef][Web of Science][Medline]
- Eddy,S.R. (2001) Non-coding RNA genes and the modern RNA world. Nature Rev. Genet., 2, 919–929.[CrossRef][Web of Science][Medline]
- Storz,G. (2002) An expanding universe of noncoding RNAs. Science, 296, 1260–1263.
[Abstract/Free Full Text] - Pace,N.R., Thomas,B.C. and Woese,C.R. (1999) Probing RNA structure, function and history by comparative analysis. In Gesteland,R.F., Cech,T.R. and Atkins,J.F. (eds), The RNA World, 2nd Edn. Cold Spring Harbor Laboratory Press, pp. 113–141.
- Pace,N.R. (1997) A molecular view of microbial diversity and the biosphere. Science, 276, 734–740.
[Abstract/Free Full Text] - 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.
[Abstract/Free Full Text] - Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673–4680.
[Abstract/Free Full Text] - Eddy,S.R. (2002) A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics, 3, 18.[CrossRef][Medline]
- Eddy,S.R. and Durbin,R. (1994) RNA sequence analysis using covariance models. Nucleic Acids Res., 22, 2079–2088.
[Abstract/Free Full Text] - Bateman,A., Birney,E., Cerruti,L., Durbin,R., Etwiller,L., Eddy,S.R., Griffiths-Jones,S., Howe,K.L., Marshall,M. and Sonnhammer,E.L.L. (2002) The Pfam protein families database. Nucleic Acids Res., 30, 276–280.
[Abstract/Free Full Text] - Wuyts,J., De Rijk,P., Van de Peer,Y., Winkelmans,T. and De Wachter,R. (2001) The European Large Subunit Ribosomal RNA Database. Nucleic Acids Res., 29, 175–177.
[Abstract/Free Full Text] - Gorodkin,J., Knudsen,B., Zwieb,C. and Samuelsson,T. (2001) SRPDB (Signal Recognition Particle Database). Nucleic Acids Res., 29, 169–170.
[Abstract/Free Full Text] - Zwieb,C. (1997) The uRNA database. Nucleic Acids Res., 25, 102–103.
[Abstract/Free Full Text] - Cannone,J.J., Subramanian,S., Schnare,M.N., Collett,J.R., D'Souza,L.M., Du,Y., Feng,B., Lin,N., Madabusi,L.V., ller,K.M., Pande,N., Shang,Z., Yu,N. and Gutell,R.R. (2002) The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics, 3, 2.[CrossRef][Medline]
- Brown,J.W. (1999) The Ribonuclease P Database. Nucleic Acids Res., 27, 314.
[Abstract/Free Full Text] - Szymanski,M., Barciszewska,M.Z., Erdmann,V.A. and Barciszewski,J. (2002) 5S Ribosomal RNA Database. Nucleic Acids Res., 30, 176–178.
[Abstract/Free Full Text] - Klosterman,P.S., Tamura,M., Holbrook,S.R. and Brenner,S.E. (2002) SCOR: a Structural Classification of RNA database. Nucleic Acids Res., 30, 392–394.
[Abstract/Free Full Text] - Maidak,B.L., Cole,J.R., Lilburn,T.G., Parker,C.T.,Jr0a, Saxman,P.R., Farris,R.J., Garrity,G.M., Olsen,G.J., Schmidt,T.M. and Tiedje,J.M. (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res., 29, 173–174.
[Abstract/Free Full Text] - van Batenburg,F.H., Gultyaev,A.P. and Pleij,C.W. (2001) PseudoBase: structural information on RNA pseudoknots. Nucleic Acids Res, 29, 194–195.
[Abstract/Free Full Text] - Wuyts,J., Van de Peer,Y., Winkelmans,T. and De Wachter,R. (2002) The European database on small subunit ribosomal RNA. Nucleic Acids Res., 30, 183–185.
[Abstract/Free Full Text] - Williams,K.P. (2002) The tmRNA Website: invasion by an intron. Nucleic Acids Res., 30, 179–182.
[Abstract/Free Full Text] - Knudsen,B., Wower,J., Zwieb,C. and Gorodkin,J. (2001) tmRDB (tmRNA database). Nucleic Acids Res., 29, 171–172.
[Abstract/Free Full Text] - 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.
[Abstract/Free Full Text] - Laslett,D., Canback,B. and Andersson,S. (2002) BRUCE: a program for the detection of transfer–messenger RNA genes in nucleotide sequences. Nucleic Acids Res., 30, 3449–3453.
[Abstract/Free Full Text] - Letunic,I., Goodstadt,L., Dickens,N.J., Doerks,T., Schultz,J., Mott,R., Ciccarelli,F., Copley,R.R., Ponting,C.P. and Bork,P. (2002) Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res., 30, 242–244.
[Abstract/Free Full Text] - Falquet,L., Pagni,M., Bucher,P., Hulo,N., Sigrist,C.J., Hofmann,K. and Bairoch,A. (2002) The PROSITE database, its status in 2002. Nucleic Acids Res., 30, 235–238.
[Abstract/Free Full Text] - Stoesser,G., Baker,W., van den Broek,A., Camon,E., Garcia-Pastor,M., Kanz,C., Kulikova,T., Leinonen,R., Lin,Q., Lombard,V., Lopez,R., Redaschi,N., Stoehr,P., Tuli,M.A., Tzouvara,K. and Vaughan,R. (2002) The EMBL Nucleotide Sequence Database. Nucleic Acids Res., 30, 21–26.
[Abstract/Free Full Text] - Shukla,G.C. and Padgett,R.A. (1999) Conservation of functional features of U6atac and U12 snRNAs between vertebrates and higher plants. RNA, 5, 525–538.[Abstract]
- Chen,J.L., Blasco,M.A. and Greider,C.W. (2000) Secondary structure of vertebrate telomerase RNA. Cell, 100, 503–514.[CrossRef][Web of Science][Medline]
- McCormick-Graham,M. and Romero,D.P. (1995) Ciliate telomerase RNA structural features. Nucleic Acids Res., 23, 1091–1097.
[Abstract/Free Full Text]
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|
|
|
|
|
A. Laederach Informatics challenges in structured RNA Brief Bioinform, September 1, 2007; 8(5): 294 - 303. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Mulhbacher and D. A. Lafontaine Ligand recognition determinants of guanine riboswitches Nucleic Acids Res., August 17, 2007; (2007) gkm572v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Freyhult, V. Moulton, and P. Clote Boltzmann probability of RNA structural neighbors and riboswitch detection Bioinformatics, August 15, 2007; 23(16): 2054 - 2062. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Blouin and D. A. Lafontaine A loop loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control RNA, August 1, 2007; 13(8): 1256 - 1267. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Freyhult, V. Moulton, and P. Clote RNAbor: a web server for RNA structural neighbors Nucleic Acids Res., July 13, 2007; 35(suppl_2): W305 - W309. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Ferre, Y. Ponty, W. A. Lorenz, and P. Clote DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities Nucleic Acids Res., July 13, 2007; 35(suppl_2): W659 - W668. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Chen, T. S. Rozhdestvensky, L. J. Collins, J. Schmitz, and D. Penny Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis Nucleic Acids Res., July 9, 2007; 35(14): 4619 - 4628. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Piccinelli and T. Samuelsson Evolution of the iron-responsive element RNA, July 1, 2007; 13(7): 952 - 966. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Kiryu, Y. Tabei, T. Kin, and K. Asai Murlet: a practical multiple alignment tool for structural RNA sequences Bioinformatics, July 1, 2007; 23(13): 1588 - 1598. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. A. Davis, M. P. S. Brown, and U. Singh Functional Characterization of Spliceosomal Introns and Identification of U2, U4, and U5 snRNAs in the Deep-Branching Eukaryote Entamoeba histolytica Eukaryot. Cell, June 1, 2007; 6(6): 940 - 948. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Lagesen, P. Hallin, E. A. Rodland, H.-H. Staerfeldt, T. Rognes, and D. W. Ussery RNAmmer: consistent and rapid annotation of ribosomal RNA genes Nucleic Acids Res., May 14, 2007; 35(9): 3100 - 3108. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Torarinsson, J. H. Havgaard, and J. Gorodkin Multiple structural alignment and clustering of RNA sequences Bioinformatics, April 15, 2007; 23(8): 926 - 932. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Zhu, D. K. Pulukkunat, and Y. Li Deciphering RNA structural diversity and systematic phylogeny from microbial metagenomes Nucleic Acids Res., April 1, 2007; 35(7): 2283 - 2294. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. St-Onge, P. Thibault, S. Hamel, and F. Major Modeling RNA tertiary structure motifs by graph-grammars Nucleic Acids Res., March 27, 2007; (2007) gkm069v2. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K.-H. Ling, M.-A. Rajandream, P. Rivailler, A. Ivens, S.-J. Yap, A. M.B.N. Madeira, K. Mungall, K. Billington, W.-Y. Yee, A. T. Bankier, et al. Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization Genome Res., March 1, 2007; 17(3): 311 - 319. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Kiryu, T. Kin, and K. Asai Robust prediction of consensus secondary structures using averaged base pairing probability matrices Bioinformatics, February 15, 2007; 23(4): 434 - 441. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Sugawara, T. Abe, T. Gojobori, and Y. Tateno DDBJ working on evaluation and classification of bacterial genes in INSDC Nucleic Acids Res., January 12, 2007; 35(suppl_1): D13 - D15. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. K. Freyhult, J. P. Bollback, and P. P. Gardner Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA Genome Res., January 1, 2007; 17(1): 117 - 125. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Lindgreen, P. P. Gardner, and A. Krogh Measuring covariation in RNA alignments: physical realism improves information measures Bioinformatics, December 15, 2006; 22(24): 2988 - 2995. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Calabrese and P. A. Sharp Characterization of the short RNAs bound by the P19 suppressor of RNA silencing in mouse embryonic stem cells RNA, December 1, 2006; 12(12): 2092 - 2102. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Voss Structural analysis of aligned RNAs Nucleic Acids Res., November 14, 2006; 34(19): 5471 - 5481. [Abstract] [Full Text] [PDF]
|
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|
|
|
S. D. Baird, M. Turcotte, R. G. Korneluk, and M. Holcik Searching for IRES RNA, October 1, 2006; 12(10): 1755 - 1785. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Mokdad and N. B. Leontis Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities Bioinformatics, September 1, 2006; 22(17): 2168 - 2170. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Tabei, K. Tsuda, T. Kin, and K. Asai SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments Bioinformatics, July 15, 2006; 22(14): 1723 - 1729. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Nishihara, A. F.A. Smit, and N. Okada Functional noncoding sequences derived from SINEs in the mammalian genome Genome Res., July 1, 2006; 16(7): 864 - 874. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Torarinsson, M. Sawera, J. H. Havgaard, M. Fredholm, and J. Gorodkin Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure Genome Res., July 1, 2006; 16(7): 885 - 889. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Bindewald, T. D. Schneider, and B. A. Shapiro CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W405 - W411. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Borenstein and E. Ruppin Direct evolution of genetic robustness in microRNA PNAS, April 25, 2006; 103(17): 6593 - 6598. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Rigoutsos, T. Huynh, K. Miranda, A. Tsirigos, A. McHardy, and D. Platt Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes PNAS, April 25, 2006; 103(17): 6605 - 6610. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Rehwinkel, P. Natalin, A. Stark, J. Brennecke, S. M. Cohen, and E. Izaurralde Genome-Wide Analysis of mRNAs Regulated by Drosha and Argonaute Proteins in Drosophila melanogaster Mol. Cell. Biol., April 15, 2006; 26(8): 2965 - 2975. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Borovok, B. Gorovitz, R. Schreiber, Y. Aharonowitz, and G. Cohen Coenzyme B12 Controls Transcription of the Streptomyces Class Ia Ribonucleotide Reductase nrdABS Operon via a Riboswitch Mechanism. J. Bacteriol., April 1, 2006; 188(7): 2512 - 2520. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. M. Burgess, D. J. Slotboom, E. R. Geertsma, R. H. Duurkens, B. Poolman, and D. van Sinderen The Riboflavin Transporter RibU in Lactococcus lactis: Molecular Characterization of Gene Expression and the Transport Mechanism. J. Bacteriol., April 1, 2006; 188(8): 2752 - 2760. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Mokdad, M. V. Krasovska, J. Sponer, and N. B. Leontis Structural and evolutionary classification of G/U wobble basepairs in the ribosome Nucleic Acids Res., March 6, 2006; 34(5): 1326 - 1341. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. BINDEWALD and B. A. SHAPIRO RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers. RNA, March 1, 2006; 12(3): 342 - 352. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Yao, Z. Weinberg, and W. L. Ruzzo CMfinder--a covariance model based RNA motif finding algorithm Bioinformatics, February 15, 2006; 22(4): 445 - 452. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. CHEN and N. RAJEWSKY Deep Conservation of MicroRNA-target Relationships and 3'UTR Motifs in Vertebrates, Flies, and Nematodes Cold Spring Harb Symp Quant Biol, January 1, 2006; 71(0): 149 - 156. [Abstract] [PDF]
|
|
|
|
|
|
S.D. GILBERT, R.K. MONTANGE, C.D. STODDARD, and R.T. BATEY Structural Studies of the Purine and SAM Binding Riboswitches Cold Spring Harb Symp Quant Biol, January 1, 2006; 71(0): 259 - 268. [Abstract] [PDF]
|
|
|
|
|
|
G. H. Jacobs, P. A. Stockwell, W. P. Tate, and C. M. Brown Transterm--extended search facilities and improved integration with other databases Nucleic Acids Res., January 1, 2006; 34(suppl_1): D37 - D40. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Kosuge, T. Abe, T. Okido, N. Tanaka, M. Hirahata, Y. Maruyama, J. Mashima, A. Tomiki, M. Kurokawa, R. Himeno, et al. Exploration and Grading of Possible Genes from 183 Bacterial Strains by a Common Protocol to Identification of New Genes: Gene Trek in Prokaryote Space (GTPS) DNA Res, January 1, 2006; 13(6): 245 - 254. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Kasprzak, E. Bindewald, and B. A. Shapiro Structural polymorphism of the HIV-1 leader region explored by computational methods Nucleic Acids Res., December 20, 2005; 33(22): 7151 - 7163. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Inagaki, K. Numata, T. Kondo, M. Tomita, K. Yasuda, A. Kanai, and Y. Kageyama Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila Genes Cells, December 1, 2005; 10(12): 1163 - 1173. [Abstract] [Full Text] [PDF]
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