multimolecule/rfam

1---2language: rna3tags:4  - Biology5  - RNA6license:7  - agpl-3.08size_categories:9  - 10M<n<100M10task_categories:11  - text-generation12  - fill-mask13task_ids:14  - language-modeling15  - masked-language-modeling16pretty_name: Rfam17library_name: multimolecule18---19 20# Rfam21 22![Rfam](https://rfam.org/static/images/rfam_logo.svg)23 24Rfam is a database of structure-annotated multiple sequence alignments, covariance models and family annotation for a number of non-coding RNA, cis-regulatory and self-splicing intron families.25 26The seed alignments are hand curated and aligned using available sequence and structure data, and covariance models are built from these alignments using the [INFERNAL v1.1.4 software suite](http://infernal.janelia.org).27 28The full regions list is created by searching the RFAMSEQ database using the covariance model, and then listing all hits above a family specific threshold to the model.29 30Rfam is maintained by a consortium of researchers at the [European Bioinformatics Institute](http://www.ebi.ac.uk), [Sean Eddy's laboratory](http://eddylab.org) and [Eric Nawrocki](https://github.com/nawrockie).31 32## Disclaimer33 34This is an UNOFFICIAL release of the [Rfam](https://rfam.org) by Ioanna Kalvari, Eric P. Nawrocki, Sarah W. Burge, Paul P Gardner, Sam Griffiths-Jones, et al.35 36**The team releasing Rfam did not write this dataset card for this dataset so this dataset card has been written by the MultiMolecule team.**37 38## Dataset Description39 40- **Homepage**: https://multimolecule.danling.org/datasets/rfam41- **Documentation**: https://docs.rfam.org/42- **datasets**: https://huggingface.co/datasets/multimolecule/rfam43- **Point of Contact**: [Blake Sweeney](https://www.ebi.ac.uk/people/person/blake-sweeney)44- **Original URL**: https://rfam.org45 46## License47 48This dataset is licensed under the [AGPL-3.0 License](https://www.gnu.org/licenses/agpl-3.0.html).49 50```spdx51SPDX-License-Identifier: AGPL-3.0-or-later52```53 54> [!TIP]55> The original Rfam dataset is licensed under the [CC0 1.0 Universal](https://creativecommons.org/publicdomain/zero/1.0) license and is available at [Rfam](https://rfam.org).56 57## Citation58 59```bibtex60@article{kalvari2021rfam,61  author    = {Kalvari, Ioanna and Nawrocki, Eric P and Ontiveros-Palacios, Nancy and Argasinska, Joanna and Lamkiewicz, Kevin and Marz, Manja and Griffiths-Jones, Sam and Toffano-Nioche, Claire and Gautheret, Daniel and Weinberg, Zasha and Rivas, Elena and Eddy, Sean R and Finn, Robert D and Bateman, Alex and Petrov, Anton I},62  copyright = {http://creativecommons.org/licenses/by/4.0/},63  journal   = {Nucleic Acids Research},64  language  = {en},65  month     = jan,66  number    = {D1},67  pages     = {D192--D200},68  publisher = {Oxford University Press (OUP)},69  title     = {Rfam 14: expanded coverage of metagenomic, viral and {microRNA} families},70  volume    = 49,71  year      = 202172}73 74@article{hufsky2021computational,75  author    = {Hufsky, Franziska and Lamkiewicz, Kevin and Almeida, Alexandre and Aouacheria, Abdel and Arighi, Cecilia and Bateman, Alex and Baumbach, Jan and Beerenwinkel, Niko and Brandt, Christian and Cacciabue, Marco and Chuguransky, Sara and Drechsel, Oliver and Finn, Robert D and Fritz, Adrian and Fuchs, Stephan and Hattab, Georges and Hauschild, Anne-Christin and Heider, Dominik and Hoffmann, Marie and H{\"o}lzer, Martin and Hoops, Stefan and Kaderali, Lars and Kalvari, Ioanna and von Kleist, Max and Kmiecinski, Ren{\'o} and K{\"u}hnert, Denise and Lasso, Gorka and Libin, Pieter and List, Markus and L{\"o}chel, Hannah F and Martin, Maria J and Martin, Roman and Matschinske, Julian and McHardy, Alice C and Mendes, Pedro and Mistry, Jaina and Navratil, Vincent and Nawrocki, Eric P and O'Toole, {\'A}ine Niamh and Ontiveros-Palacios, Nancy and Petrov, Anton I and Rangel-Pineros, Guillermo and Redaschi, Nicole and Reimering, Susanne and Reinert, Knut and Reyes, Alejandro and Richardson, Lorna and Robertson, David L and Sadegh, Sepideh and Singer, Joshua B and Theys, Kristof and Upton, Chris and Welzel, Marius and Williams, Lowri and Marz, Manja},76  copyright = {http://creativecommons.org/licenses/by/4.0/},77  journal   = {Briefings in Bioinformatics},78  month     = mar,79  number    = 2,80  pages     = {642--663},81  publisher = {Oxford University Press (OUP)},82  title     = {Computational strategies to combat {COVID-19}: useful tools to accelerate {SARS-CoV-2} and coronavirus research},83  volume    = 22,84  year      = 202185}86 87@article{kalvari2018noncoding,88  author  = {Kalvari, Ioanna and Nawrocki, Eric P and Argasinska, Joanna and Quinones-Olvera, Natalia and Finn, Robert D and Bateman, Alex and Petrov, Anton I},89  journal = {Current Protocols in Bioinformatics},90  month   = jun,91  number  = 1,92  pages   = {e51},93  title   = {Non-coding {RNA} analysis using the rfam database},94  volume  = 62,95  year    = 201896}97 98@article{kalvari2018rfam,99  author  = {Kalvari, Ioanna and Argasinska, Joanna and Quinones-Olvera,100             Natalia and Nawrocki, Eric P and Rivas, Elena and Eddy, Sean R101             and Bateman, Alex and Finn, Robert D and Petrov, Anton I},102  journal = {Nucleic Acids Research},103  month   = jan,104  number  = {D1},105  pages   = {D335--D342},106  title   = {Rfam 13.0: shifting to a genome-centric resource for non-coding {RNA} families},107  volume  = 46,108  year    = 2018109}110 111@article{nawrocki2015rfam,112  author    = {Nawrocki, Eric P and Burge, Sarah W and Bateman, Alex and Daub, Jennifer and Eberhardt, Ruth Y and Eddy, Sean R and Floden, Evan W and Gardner, Paul P and Jones, Thomas A and Tate, John and Finn, Robert D},113  copyright = {http://creativecommons.org/licenses/by/4.0/},114  journal   = {Nucleic Acids Research},115  month     = jan,116  number    = {Database issue},117  pages     = {D130--7},118  publisher = {Oxford University Press (OUP)},119  title     = {Rfam 12.0: updates to the {RNA} families database},120  volume    = 43,121  year      = 2015122}123 124@article{burge2013rfam,125  author    = {Burge, Sarah W and Daub, Jennifer and Eberhardt, Ruth and Tate, John and Barquist, Lars and Nawrocki, Eric P and Eddy, Sean R and Gardner, Paul P and Bateman, Alex},126  copyright = {http://creativecommons.org/licenses/by-nc/3.0/},127  journal   = {Nucleic Acids Research},128  month     = jan,129  number    = {Database issue},130  pages     = {D226--32},131  publisher = {Oxford University Press (OUP)},132  title     = {Rfam 11.0: 10 years of {RNA} families},133  volume    = 41,134  year      = 2013135}136 137@article{gardner2011rfam,138  author  = {Gardner, Paul P and Daub, Jennifer and Tate, John and Moore, Benjamin L and Osuch, Isabelle H and Griffiths-Jones, Sam and Finn, Robert D and Nawrocki, Eric P and Kolbe, Diana L and Eddy, Sean R and Bateman, Alex},139  journal = {Nucleic Acids Research},140  month   = jan,141  number  = {Database issue},142  pages   = {D141--5},143  title   = {Rfam: Wikipedia, clans and the ``decimal'' release},144  volume  = 39,145  year    = 2011146}147 148@article{gardner2009rfam,149  author   = {Gardner, Paul P and Daub, Jennifer and Tate, John G and Nawrocki, Eric P and Kolbe, Diana L and Lindgreen, Stinus and Wilkinson, Adam C and Finn, Robert D and Griffiths-Jones, Sam and Eddy, Sean R and Bateman, Alex},150  journal  = {Nucleic Acids Research},151  month    = jan,152  number   = {Database issue},153  pages    = {D136--40},154  title    = {Rfam: updates to the {RNA} families database},155  volume   = 37,156  year     = 2009157}158 159@article{daub2008rna,160  author   = {Daub, Jennifer and Gardner, Paul P and Tate, John and Ramsk{\"o}ld, Daniel and Manske, Magnus and Scott, William G and Weinberg, Zasha and Griffiths-Jones, Sam and Bateman, Alex},161  journal  = {RNA},162  month    = dec,163  number   = 12,164  pages    = {2462--2464},165  title    = {The {RNA} {WikiProject}: community annotation of {RNA} families},166  volume   = 14,167  year     = 2008168}169 170@article{griffiths2005rfam,171  author   = {Griffiths-Jones, Sam and Moxon, Simon and Marshall, Mhairi and Khanna, Ajay and Eddy, Sean R. and Bateman, Alex},172  doi      = {10.1093/nar/gki081},173  eprint   = {https://academic.oup.com/nar/article-pdf/33/suppl\_1/D121/7622063/gki081.pdf},174  issn     = {0305-1048},175  journal  = {Nucleic Acids Research},176  month    = jan,177  number   = {suppl_1},178  pages    = {D121-D124},179  title    = {{Rfam: annotating non-coding RNAs in complete genomes}},180  url      = {https://doi.org/10.1093/nar/gki081},181  volume   = {33},182  year     = {2005}183}184 185@article{griffiths2003rfam,186  author   = {Griffiths-Jones, Sam and Bateman, Alex and Marshall, Mhairi and Khanna, Ajay and Eddy, Sean R.},187  doi      = {10.1093/nar/gkg006},188  eprint   = {https://academic.oup.com/nar/article-pdf/31/1/439/7125749/gkg006.pdf},189  issn     = {0305-1048},190  journal  = {Nucleic Acids Research},191  month    = jan,192  number   = {1},193  pages    = {439-441},194  title    = {{Rfam: an RNA family database}},195  url      = {https://doi.org/10.1093/nar/gkg006},196  volume   = {31},197  year     = {2003}198}199```200