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1. RNAcentral: A comprehensive database of non-coding RNA sequences

Author

Petrov, AI, Kay, SJE, Kalvari, I, Howe, KL, Gray, KA, Bruford, EA, Kersey, PJ, Cochrane, G, Finn, RD, Bateman, A, Kozomara, A, Griffiths-Jones, S, Frankish, A, Zwieb, CW, Lau, BY, Williams, KP, Chan, PP, Lowe, TM, Cannone, JJ, Gutell, RR, Machnicka, MA, Bujnicki, JM, Yoshihama, M, Kenmochi, N, Chai, B, Cole, JR, Szymanski, M, Karlowski, WM, Wood, V, Huala, E, Berardini, TZ, Zhao, Y, Chen, R, Zhu, W, Paraskevopoulou, MD, Vlachos, IS, Hatzigeorgiou, AG, Ma, L, Zhang, Z, Puetz, J, Stadler, PF, McDonald, D, Basu, S, Fey, P, Engel, SR, Cherry, JM, Volders, PJ, Mestdagh, P, Wower, J, Clark, M, Quek, XC, Dinger, ME, Petrov, AI, Kay, SJE, Kalvari, I, Howe, KL, Gray, KA, Bruford, EA, Kersey, PJ, Cochrane, G, Finn, RD, Bateman, A, Kozomara, A, Griffiths-Jones, S, Frankish, A, Zwieb, CW, Lau, BY, Williams, KP, Chan, PP, Lowe, TM, Cannone, JJ, Gutell, RR, Machnicka, MA, Bujnicki, JM, Yoshihama, M, Kenmochi, N, Chai, B, Cole, JR, Szymanski, M, Karlowski, WM, Wood, V, Huala, E, Berardini, TZ, Zhao, Y, Chen, R, Zhu, W, Paraskevopoulou, MD, Vlachos, IS, Hatzigeorgiou, AG, Ma, L, Zhang, Z, Puetz, J, Stadler, PF, McDonald, D, Basu, S, Fey, P, Engel, SR, Cherry, JM, Volders, PJ, Mestdagh, P, Wower, J, Clark, M, Quek, XC, and Dinger, ME

Abstract

© The Author(s) 2016. RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/.

Published
2017

2. RNAcentral: a comprehensive database of non-coding RNA sequences

Author

Petrov, AI, Kay, SJE, Kalvari, I, Howe, KL, Gray, KA, Bruford, EA, Kersey, PJ, Cochrane, G, Finn, RD, Bateman, A, Kozomara, A, Griffiths-Jones, S, Frankish, A, Zwieb, CW, Lau, BY, Williams, KP, Chan, PP, Lowe, TM, Cannone, JJ, Gutell, RR, Machnicka, MA, Bujnicki, JM, Yoshihama, M, Kenmochi, N, Chai, B, Cole, JR, Szymanski, M, Karlowski, WM, Wood, V, Huala, E, Berardini, TZ, Zhao, Y, Chen, R, Zhu, W, Paraskevopoulou, MD, Vlachos, IS, Hatzigeorgiou, AG, Ma, L, Zhang, Z, Puetz, J, Stadler, PF, McDonald, D, Basu, S, Fey, P, Engel, SR, Cherry, JM, Volders, PJ, Mestdagh, P, Wower, J, Clark, M, Quek, XC, Dinger, ME, Bruford, Elspeth [0000-0002-8380-5247], Wood, Valerie [0000-0001-6330-7526], and Apollo - University of Cambridge Repository

Subjects
EXPRESSION, 0301 basic medicine, RNA, Untranslated, MICRORNAS, Sequence analysis, Genomics, Context (language use), Biology, computer.software_genre, Data type, Genome, 03 medical and health sciences, Species Specificity, TARGETS, RESOURCE, REVEALS, TRANSCRIPTS, Genetics, Database Issue, Animals, Humans, GENOME DATABASE, LANDSCAPE, Database, Nucleotides, Sequence Analysis, RNA, Biology and Life Sciences, Subject (documents), Non-coding RNA, GENE DATABASE, Identifier, 030104 developmental biology, UPDATE, Databases, Nucleic Acid, computer
Abstract

RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/.

Published
2016

3. RNAcentral: An international database of ncRNA sequences

Author

Petrov, AI, Kay, SJE, Gibson, R, Kulesha, E, Staines, D, Bruford, EA, Wright, MW, Burge, S, Finn, RD, Kersey, PJ, Cochrane, G, Bateman, A, Griffiths-Jones, S, Harrow, J, Chan, PP, Lowe, TM, Zwieb, CW, Wower, J, Williams, KP, Hudson, CM, Gutell, R, Clark, MB, Dinger, M, Quek, XC, Bujnicki, JM, Chua, NH, Liu, J, Wang, H, Skogerbø, G, Zhao, Y, Chen, R, Zhu, W, Cole, JR, Chai, B, Huang, HD, Huang, HY, Cherry, JM, Hatzigeorgiou, A, Pruitt, KD, Petrov, AI, Kay, SJE, Gibson, R, Kulesha, E, Staines, D, Bruford, EA, Wright, MW, Burge, S, Finn, RD, Kersey, PJ, Cochrane, G, Bateman, A, Griffiths-Jones, S, Harrow, J, Chan, PP, Lowe, TM, Zwieb, CW, Wower, J, Williams, KP, Hudson, CM, Gutell, R, Clark, MB, Dinger, M, Quek, XC, Bujnicki, JM, Chua, NH, Liu, J, Wang, H, Skogerbø, G, Zhao, Y, Chen, R, Zhu, W, Cole, JR, Chai, B, Huang, HD, Huang, HY, Cherry, JM, Hatzigeorgiou, A, and Pruitt, KD

Abstract

The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNA-central, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

Published
2015

4. RNAcentral: a comprehensive database of non-coding RNA sequences.

Author

Petrov AI, Kay SJE, Kalvari I, Howe KL, Gray KA, Bruford EA, Kersey PJ, Cochrane G, Finn RD, Bateman A, Kozomara A, Griffiths-Jones S, Frankish A, Zwieb CW, Lau BY, Williams KP, Chan PP, Lowe TM, Cannone JJ, Gutell R, Machnicka MA, Bujnicki JM, Yoshihama M, Kenmochi N, Chai B, Cole JR, Szymanski M, Karlowski WM, Wood V, Huala E, Berardini TZ, Zhao Y, Chen R, Zhu W, Paraskevopoulou MD, Vlachos IS, Hatzigeorgiou AG, Ma L, Zhang Z, Puetz J, Stadler PF, McDonald D, Basu S, Fey P, Engel SR, Cherry JM, Volders PJ, Mestdagh P, Wower J, Clark MB, Quek XC, and Dinger ME

Subjects
Animals, Genomics, Humans, Nucleotides chemistry, Sequence Analysis, RNA, Species Specificity, Databases, Nucleic Acid, RNA, Untranslated chemistry
Abstract

RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/., (© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2017
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5. RNAcentral: an international database of ncRNA sequences.

Author

Petrov AI, Kay SJE, Gibson R, Kulesha E, Staines D, Bruford EA, Wright MW, Burge S, Finn RD, Kersey PJ, Cochrane G, Bateman A, Griffiths-Jones S, Harrow J, Chan PP, Lowe TM, Zwieb CW, Wower J, Williams KP, Hudson CM, Gutell R, Clark MB, Dinger M, Quek XC, Bujnicki JM, Chua NH, Liu J, Wang H, Skogerbø G, Zhao Y, Chen R, Zhu W, Cole JR, Chai B, Huang HD, Huang HY, Cherry JM, Hatzigeorgiou A, and Pruitt KD

Subjects
Chromosome Mapping, Humans, Internet, RNA, Untranslated genetics, Sequence Analysis, RNA, Databases, Nucleic Acid, RNA, Untranslated chemistry
Abstract

The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species., (© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2015
Full Text
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