For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
83
views
41
references
 Top references
cited by
23
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      6
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Rfam: Wikipedia, clans and the “decimal” release

      research-article

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models. In this contribution, we discuss the pros and cons of using the online encyclopedia, Wikipedia, as a source of community‐derived annotation. We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at http://rfam.sanger.ac.uk.

          Related collections

          Most cited references41

          • Record: found
          • Abstract: found
          • Article: not found

          Gene Ontology: tool for the unification of biology

          Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)
          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
          Article 0 comments Cited 15226 times – based on 0 reviews     Review now
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Pfam: clans, web tools and services

            Robert D. Finn, Jaina Mistry, Benjamin Schuster-Böckler … (2005)
            Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are described in detail, together with the new associated web pages. Improvements to the range of Pfam web tools and the first set of Pfam web services that allow programmatic access to the database and associated tools are also presented. Pfam is available on the web in the UK (), the USA (), France () and Sweden ().
            Article 0 comments Cited 680 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Rfam: an RNA family database.

              S. Griffiths-Jones (2003)
              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.
              Article 0 comments Cited 624 times – based on 0 reviews     Review now
                Bookmark
                All references

                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Journal ID (hwp): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: January 2011
                Publication date (Print): January 2011
                Publication date (Electronic): 8 November 2010
                Publication date PMC-release: 8 November 2010
                Volume: 39
                Issue: Database issue , Database issue
                Pages: D141-D145
                Affiliations
                1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA0, 2Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, UK and 3Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
                Author notes
                *To whom correspondence should be addressed. Tel: +44 1223 494 726; Fax: +44 1223 494 919; Email: pg5@ 123456sanger.ac.uk
                Correspondence may be also be addressed to Alex Bateman. Tel: +44 1223 494950; Fax: +44 1223 494919; Email: agb@ 123456sanger.ac.uk
                Article
                Publisher ID: gkq1129
                DOI: 10.1093/nar/gkq1129
                PMC ID: 3013711
                PubMed ID: 21062808
                SO-VID: e16c8813-0c44-40aa-b98f-9cb8cb686956
                Copyright © © The Author(s) 2010. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 15 September 2010
                Date revision received : 20 October 2010
                Date accepted : 21 October 2010
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

                Comments

                Comment on this article