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An RNA motifs database
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# RMfam: multiple alignments and probabilistic models of RNA motifs. ### Release 0.3 0. CONTENTS 1. INTRODUCTION 2. AVAILABILITY 3. FILES 4. HISTORY 5. HOW TO CITE RMFAM ## 1. INTRODUCTION RMfam is a database of annotated multiple sequence alignments and probabilistic models for a number of RNA motifs. For the purposes of this work an RNA motif is a recurring RNA sequence and/or secondary structure found within larger structures that can be modelled by either a covariance model or a profile HMM. RMfam is modelled loosely on the Rfam and Pfam databases and draws a lot of ideas from these resources. RMfam is licensed under a Creative Commons Attribution 3.0 Unported License (http://creativecommons.org/licenses/by/3.0/). ## 2. AVAILABILITY RMfam is available on the web at the following URL: `https://github.com/ppgardne` ## 3. FILES <pre> README - this file USERMAN - a description of the RMfam flatfile formats LICENSE - Legalese stating RMfam's copyright is CC BY 3.0 */SEED - Annotated alignment files of motifs (named *) RMfam.cm - a concatenated set of RMfam covariance models in ascii INFERNAL format Rfam.stk - Rfam seed alignments in STOCKHOLM format that have been annotated with RMfam motifs Rfam.tab - A table of mappings between RMfam and Rfam. The format is: --column 1: Rfam accessions --column 2: Rfam ID --column 3: RMfam ID --column 4: fraction of sequences in Rfam seed that contain the RMfam motif --column 5: sum of bit scores --column 6: weighted sum of bit scores (using GSC tree weights from esl-weights, weight the sum of bits, normalise with the total weights). I.e. (\sum_i (w_i * bits_i))/( \sum_i w_i ) PDB.gff - Annotations of nucleotide sequences derived from PDB entries accessions.txt - Tab-delimited file of RMfam accessions and corresponding IDs rmfam_scan.pl - A script for annotating sequences and alignments with RMfam families </pre> ## 4. HISTORY <pre> Version Date # families Rfam PDB ------- ---- ---------- ------- ----- 0.1 10/11 14 Rfam 10.1 03/11/11 0.2 05/12 24 Rfam 10.1 03/11/11 0.3 06/14 34 Rfam 11.0 01/06/14 </pre> ## 5. HOW TO CITE RMfam If you make use of RMfam in your work we ask that you cite the following publications: `Gardner PP and Eldai H (2015) Annotating RNA motifs in sequences and alignments. Nucl. Acids Res. 43 (2): 691-698.` Feb 2016