DOI: 10.1093/bioinformatics/btp250. VARNA: Interactive drawing and editing of the RNA secondary structure

VARNA: Interactive drawing and editing of the RNA secondary structure

10.1093/bioinformatics/btp250

Crossref journal-article

Oxford University Press (OUP)

Bioinformatics (286)

Abstract

Abstract Description: VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Features: VARNA implements four drawing algorithms, supports input/output using the classic formats dbn, ct, bpseq and RNAML and exports the drawing as five picture formats, either pixel-based (JPEG, PNG) or vector-based (SVG, EPS and XFIG). It also allows manual modification and structural annotation of the resulting drawing using either an interactive point and click approach, within a web server or through command-line arguments. Availability: VARNA is a free software, released under the terms of the GPLv3.0 license and available at http://varna.lri.fr Contact: ponty@lri.fr Supplementary information: Supplementary data are available at Bioinformatics online.

Bibliography

Darty, K., Denise, A., & Ponty, Y. (2009). VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25(15), 1974â1975.

Authors 3

Kévin Darty (first)
Alain Denise (additional)
Yann Ponty (additional)

References 11 Referenced 1,145

{'key': '2023013112100484400_B1', 'article-title': 'Alignment of RNA structures', 'author': 'Blin', 'year': '2008', 'journal-title': 'IEEE/ACM Trans. Comput. Biol. Bioinform.'} / IEEE/ACM Trans. Comput. Biol. Bioinform. / Alignment of RNA structures by Blin (2008)
{'key': '2023013112100484400_B2', 'first-page': '167', 'article-title': 'An improved algorithm for nucleic acid secondary structure display', 'volume': '4', 'author': 'Bruccoleri', 'year': '1988', 'journal-title': 'Comput. Appl. Biosci.'} / Comput. Appl. Biosci. / An improved algorithm for nucleic acid secondary structure display by Bruccoleri (1988)
{'key': '2023013112100484400_B3', 'article-title': 'The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs', 'volume': '3', 'author': 'Cannone', 'year': '2002', 'journal-title': 'BMC Bioinformatics'} / BMC Bioinformatics / The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs by Cannone (2002)
10.1093/nar/gkh449 / Nucleic Acids Res. / SFold web server for statistical folding and rational design of nucleic acids by Ding (2004)
10.1017/S1355838201002515 / RNA / Geometric nomenclature and classification of RNA base pairs by Leontis (2001)
10.1093/nar/gki591 / Nucleic Acids Res. / Dinamelt web server for nucleic acid melting prediction by Markham (2005)
10.1093/nar/gkj081 / Nucleic Acids Res. / IRESite: the database of experimentally verified IRES structures (www.iresite.org) by Mokrejs (2006)
10.1093/bioinformatics/19.2.299 / Bioinformatics / Rnaviz2: an improved representation of RNA secondary structure by Rijk (2003)
10.1073/pnas.0409169102 / Proc. Natl Acad. Sci. USA / Fast and reliable prediction of noncoding RNAs by Washietl (2005)
10.1017/S1355838202028017 / RNA / RNAML: a standard syntax for exchanging RNA information by Waugh (2002)
10.1073/pnas.2536430100 / Proc. Natl Acad. Sci. USA / Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations by Xayaphoummine (2003)

Dates

Type	When
Created	16 years, 3 months ago (April 27, 2009, 8:25 p.m.)
Deposited	2 years, 6 months ago (Jan. 31, 2023, 4:31 p.m.)
Indexed	4 days, 1 hour ago (Aug. 21, 2025, 12:33 p.m.)
Issued	16 years, 3 months ago (April 27, 2009)
Published	16 years, 3 months ago (April 27, 2009)
Published Online	16 years, 3 months ago (April 27, 2009)
Published Print	16 years ago (Aug. 1, 2009)

Funders 0

None

BibTeX

@article{Darty_2009, title={VARNA: Interactive drawing and editing of the RNA secondary structure}, volume={25}, ISSN={1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/btp250}, DOI={10.1093/bioinformatics/btp250}, number={15}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Darty, Kévin and Denise, Alain and Ponty, Yann}, year={2009}, month=apr, pages={1974–1975} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        8,
        21
      ]
    ],
    "date-time": "2025-08-21T16:33:04Z",
    "timestamp": 1755793984094
  },
  "reference-count": 11,
  "publisher": "Oxford University Press (OUP)",
  "issue": "15",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2016,
            10,
            2
          ]
        ],
        "date-time": "2016-10-02T00:00:00Z",
        "timestamp": 1475366400000
      },
      "content-version": "vor",
      "delay-in-days": 2715,
      "URL": "http://creativecommons.org/licenses/by-nc/2.0/uk/"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2009,
        8,
        1
      ]
    ]
  },
  "abstract": "<jats:title>Abstract</jats:title>\n               <jats:p>Description: \u00a0VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.</jats:p>\n               <jats:p>Features: \u00a0VARNA implements four drawing algorithms, supports input/output using the classic formats dbn, ct, bpseq and RNAML and exports the drawing as five picture formats, either pixel-based (JPEG, PNG) or vector-based (SVG, EPS and XFIG). It also allows manual modification and structural annotation of the resulting drawing using either an interactive point and click approach, within a web server or through command-line arguments.</jats:p>\n               <jats:p>Availability: \u00a0VARNA is a free software, released under the terms of the GPLv3.0 license and available at http://varna.lri.fr</jats:p>\n               <jats:p>Contact: \u00a0ponty@lri.fr</jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.</jats:p>",
  "DOI": "10.1093/bioinformatics/btp250",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2009,
        4,
        28
      ]
    ],
    "date-time": "2009-04-28T00:25:20Z",
    "timestamp": 1240878320000
  },
  "page": "1974-1975",
  "source": "Crossref",
  "is-referenced-by-count": 1145,
  "title": "VARNA: Interactive drawing and editing of the RNA secondary structure",
  "prefix": "10.1093",
  "volume": "25",
  "author": [
    {
      "given": "K\u00e9vin",
      "family": "Darty",
      "sequence": "first",
      "affiliation": [
        {
          "name": "1 LRI, UMR CNRS 8623, 2 IGM, UMR CNRS 8621, Universit\u00e9 Paris-Sud 11 F91405 Orsay cedex and 3 G\u00e9nomique Analytique, INSERM U511, 75013 Paris, France"
        }
      ]
    },
    {
      "given": "Alain",
      "family": "Denise",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "1 LRI, UMR CNRS 8623, 2 IGM, UMR CNRS 8621, Universit\u00e9 Paris-Sud 11 F91405 Orsay cedex and 3 G\u00e9nomique Analytique, INSERM U511, 75013 Paris, France"
        },
        {
          "name": "1 LRI, UMR CNRS 8623, 2 IGM, UMR CNRS 8621, Universit\u00e9 Paris-Sud 11 F91405 Orsay cedex and 3 G\u00e9nomique Analytique, INSERM U511, 75013 Paris, France"
        }
      ]
    },
    {
      "given": "Yann",
      "family": "Ponty",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "1 LRI, UMR CNRS 8623, 2 IGM, UMR CNRS 8621, Universit\u00e9 Paris-Sud 11 F91405 Orsay cedex and 3 G\u00e9nomique Analytique, INSERM U511, 75013 Paris, France"
        },
        {
          "name": "1 LRI, UMR CNRS 8623, 2 IGM, UMR CNRS 8621, Universit\u00e9 Paris-Sud 11 F91405 Orsay cedex and 3 G\u00e9nomique Analytique, INSERM U511, 75013 Paris, France"
        }
      ]
    }
  ],
  "member": "286",
  "published-online": {
    "date-parts": [
      [
        2009,
        4,
        27
      ]
    ]
  },
  "reference": [
    {
      "key": "2023013112100484400_B1",
      "article-title": "Alignment of RNA structures",
      "author": "Blin",
      "year": "2008",
      "journal-title": "IEEE/ACM Trans. Comput. Biol. Bioinform."
    },
    {
      "key": "2023013112100484400_B2",
      "first-page": "167",
      "article-title": "An improved algorithm for nucleic acid secondary structure display",
      "volume": "4",
      "author": "Bruccoleri",
      "year": "1988",
      "journal-title": "Comput. Appl. Biosci."
    },
    {
      "key": "2023013112100484400_B3",
      "article-title": "The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs",
      "volume": "3",
      "author": "Cannone",
      "year": "2002",
      "journal-title": "BMC Bioinformatics"
    },
    {
      "issue": "Web Server Issue",
      "key": "2023013112100484400_B4",
      "doi-asserted-by": "crossref",
      "first-page": "135",
      "DOI": "10.1093/nar/gkh449",
      "article-title": "SFold web server for statistical folding and rational design of nucleic acids",
      "volume": "32",
      "author": "Ding",
      "year": "2004",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "2023013112100484400_B5",
      "doi-asserted-by": "crossref",
      "first-page": "499",
      "DOI": "10.1017/S1355838201002515",
      "article-title": "Geometric nomenclature and classification of RNA base pairs",
      "volume": "7",
      "author": "Leontis",
      "year": "2001",
      "journal-title": "RNA"
    },
    {
      "key": "2023013112100484400_B6",
      "doi-asserted-by": "crossref",
      "first-page": "577",
      "DOI": "10.1093/nar/gki591",
      "article-title": "Dinamelt web server for nucleic acid melting prediction",
      "volume": "33",
      "author": "Markham",
      "year": "2005",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "2023013112100484400_B7",
      "doi-asserted-by": "crossref",
      "first-page": "D125",
      "DOI": "10.1093/nar/gkj081",
      "article-title": "IRESite: the database of experimentally verified IRES structures (www.iresite.org)",
      "volume": "34",
      "author": "Mokrejs",
      "year": "2006",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "2023013112100484400_B8",
      "doi-asserted-by": "crossref",
      "first-page": "299",
      "DOI": "10.1093/bioinformatics/19.2.299",
      "article-title": "Rnaviz2: an improved representation of RNA secondary structure",
      "volume": "2",
      "author": "Rijk",
      "year": "2003",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "2023013112100484400_B9",
      "doi-asserted-by": "crossref",
      "first-page": "2454",
      "DOI": "10.1073/pnas.0409169102",
      "article-title": "Fast and reliable prediction of noncoding RNAs",
      "volume": "102",
      "author": "Washietl",
      "year": "2005",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "2023013112100484400_B10",
      "doi-asserted-by": "crossref",
      "first-page": "707",
      "DOI": "10.1017/S1355838202028017",
      "article-title": "RNAML: a standard syntax for exchanging RNA information",
      "volume": "8",
      "author": "Waugh",
      "year": "2002",
      "journal-title": "RNA"
    },
    {
      "key": "2023013112100484400_B11",
      "doi-asserted-by": "crossref",
      "first-page": "15310",
      "DOI": "10.1073/pnas.2536430100",
      "article-title": "Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations",
      "volume": "100",
      "author": "Xayaphoummine",
      "year": "2003",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    }
  ],
  "container-title": "Bioinformatics",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://academic.oup.com/bioinformatics/article-pdf/25/15/1974/48994552/bioinformatics_25_15_1974.pdf",
      "content-type": "application/pdf",
      "content-version": "vor",
      "intended-application": "syndication"
    },
    {
      "URL": "https://academic.oup.com/bioinformatics/article-pdf/25/15/1974/48994552/bioinformatics_25_15_1974.pdf",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2023,
        1,
        31
      ]
    ],
    "date-time": "2023-01-31T21:31:31Z",
    "timestamp": 1675200691000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://academic.oup.com/bioinformatics/article/25/15/1974/210730"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2009,
        4,
        27
      ]
    ]
  },
  "references-count": 11,
  "journal-issue": {
    "issue": "15",
    "published-print": {
      "date-parts": [
        [
          2009,
          8,
          1
        ]
      ]
    }
  },
  "URL": "http://dx.doi.org/10.1093/bioinformatics/btp250",
  "relation": {},
  "ISSN": [
    "1367-4811",
    "1367-4803"
  ],
  "subject": [],
  "published-other": {
    "date-parts": [
      [
        2009,
        8,
        1
      ]
    ]
  },
  "published": {
    "date-parts": [
      [
        2009,
        4,
        27
      ]
    ]
  }
}