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Items: 1 to 20 of 100

1.

Rfam: Wikipedia, clans and the "decimal" release.

Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A.

Nucleic Acids Res. 2011 Jan;39(Database issue):D141-5. doi: 10.1093/nar/gkq1129.

2.

Rfam 11.0: 10 years of RNA families.

Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A.

Nucleic Acids Res. 2013 Jan;41(Database issue):D226-32. doi: 10.1093/nar/gks1005.

3.

Rfam: an RNA family database.

Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR.

Nucleic Acids Res. 2003 Jan 1;31(1):439-41.

4.

Rfam: annotating non-coding RNAs in complete genomes.

Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D121-4.

5.

Rfam 12.0: updates to the RNA families database.

Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD.

Nucleic Acids Res. 2015 Jan;43(Database issue):D130-7. doi: 10.1093/nar/gku1063.

6.

Rfam: updates to the RNA families database.

Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D136-40. doi: 10.1093/nar/gkn766.

7.

Rfam: annotating families of non-coding RNA sequences.

Daub J, Eberhardt RY, Tate JG, Burge SW.

Methods Mol Biol. 2015;1269:349-63. doi: 10.1007/978-1-4939-2291-8_22.

PMID:
25577390
8.

CMCompare webserver: comparing RNA families via covariance models.

Eggenhofer F, Hofacker IL, Höner Zu Siederdissen C.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W499-503. doi: 10.1093/nar/gkt329.

9.

The RNA WikiProject: community annotation of RNA families.

Daub J, Gardner PP, Tate J, Ramsköld D, Manske M, Scott WG, Weinberg Z, Griffiths-Jones S, Bateman A.

RNA. 2008 Dec;14(12):2462-4. doi: 10.1261/rna.1200508.

10.

Crowdsourcing RNA structural alignments with an online computer game.

Waldispühl J, Kam A, Gardner PP.

Pac Symp Biocomput. 2015:330-41.

11.

Ambivalent covariance models.

Janssen S, Giegerich R.

BMC Bioinformatics. 2015 May 28;16:178. doi: 10.1186/s12859-015-0569-1.

12.

Annotating non-coding RNAs with Rfam.

Griffiths-Jones S.

Curr Protoc Bioinformatics. 2005 Apr;Chapter 12:Unit 12.5. doi: 10.1002/0471250953.bi1205s9.

PMID:
18428745
13.

BlastR--fast and accurate database searches for non-coding RNAs.

Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E, Bucher P, Notredame C.

Nucleic Acids Res. 2011 Sep 1;39(16):6886-95. doi: 10.1093/nar/gkr335.

14.

Software.ncrna.org: web servers for analyses of RNA sequences.

Asai K, Kiryu H, Hamada M, Tabei Y, Sato K, Matsui H, Sakakibara Y, Terai G, Mituyama T.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W75-8. doi: 10.1093/nar/gkn222.

15.

Identification and classification of ncRNA molecules using graph properties.

Childs L, Nikoloski Z, May P, Walther D.

Nucleic Acids Res. 2009 May;37(9):e66. doi: 10.1093/nar/gkp206.

16.

Clustering rfam 10.1: clans, families, and classes.

Lessa FA, Raiol T, Brigido MM, Martins Neto DS, Walter ME, Stadler PF.

Genes (Basel). 2012 Jul 5;3(3):378-90. doi: 10.3390/genes3030378.

17.

Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering.

Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R.

PLoS Comput Biol. 2007 Apr 13;3(4):e65.

18.

Customized strategies for discovering distant ncRNA homologs.

Mosig A, Zhu L, Stadler PF.

Brief Funct Genomic Proteomic. 2009 Nov;8(6):451-60. doi: 10.1093/bfgp/elp035. Review.

19.

Structural alignment of RNA with complex pseudoknot structure.

Wong TK, Lam TW, Sung WK, Cheung BW, Yiu SM.

J Comput Biol. 2011 Jan;18(1):97-108. doi: 10.1089/cmb.2009.0275.

PMID:
21210732
20.

The Pfam protein families database.

Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD.

Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301. doi: 10.1093/nar/gkr1065.

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