Rfam: Wikipedia, clans and the "decimal" release

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.

Figure 1.

Edits for Wikipedia articles on RNA families. The cumulative number of edits since 1st January 2007 for the 733 Wikipedia articles that are associated with Rfam entries is shown in black. The total number of edits that were reverted or labeled as vandalism is shown in red. To mid-2010, there were just 106 of these. However, some reverted edits may have been well-intentioned but were deemed inappropriate for Wikipedia.

Figure 2.

An example Stockholm alignment for the UPSK pseudoknot from turnip yellow mosaic virus. The Stockholm alignment format is flexible enough to allow generic mark-up of file information with ‘#=GF' lines, sequence information with ‘#=GS' lines and column information with ‘#=GC' lines. Each is followed by at least a two-letter code giving an indication for what follows e.g. ‘ID' implies ‘identifier', ‘AC' implies ‘accession', ‘AU' implies ‘author', etc. All the commonly used tags are documented in the Wikipedia article for Stockholm alignment (25).