Rfam database of RNA families

Sam Griffiths-Jones sgj at sanger.ac.uk
Fri Nov 29 09:41:53 EST 2002


Rfam: A new database of multiple alignments and covariance models of
non-coding RNA families
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Rfam is a database of structure-annotated multiple sequence
alignments, covariance models and family annotation for a number of
non-coding RNA families.  Rfam 2.0 contains 30 such families.  The
seed alignments are hand curated and aligned using available data, and
covariance models are built from these alignments using the INFERNAL
0.52 software suite (http://infernal.wustl.edu/).  The full alignments
are created by searching a subset of the EMBL nucleotide database
using the covariance model, and then aligning all hits above a family
specific threshold to the model.  Rfam 2.0 annotates 65072 regions in
the EMBL database.

Rfam is available on the web at the following URLs:

http://www.sanger.ac.uk/Software/Rfam/
http://rfam.wustl.edu/

The database is also available for download in flatfile format from:

ftp://ftp.sanger.ac.uk/pub/databases/Rfam/
ftp://ftp.genetics.wustl.edu/pub/eddy/Rfam/

For local searching the INFERNAL package is also required:

http://infernal.wustl.edu/

Rfam is maintained by a consortium of researchers at the Wellcome
Trust Sanger Institute, Cambridge, UK, and Washington University, St.
Louis, USA.

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November 2002 - The Rfam Consortium






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