RNA DATABASES

Rfam

(http://rfam.sanger.ac.uk/)

Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs). The primary aim of Rfam is to annotate new members of known RNA families on nucleotide sequences, particularly complete genomes, using sensitive BLAST filters in combination with CMs. Rfam release 9.0 contains 603 families, each represented by a multiple sequence alignment of known and predicted representative members of the family, annotated with a consensus base-paired secondary structure

Seed alignment for the U12 spliceosomal RNA family. Secondary structure base pairs are encoded in the coloured bases in the alignment,

An example of the new secondary markups used by Rfam. The coronavirus 30-UTR pseudo knot is shown (Rfam Accession RF00165sequence conservation (A), covariation (B), base-pair conservation also known as the fraction of canonical base pairs (C) and CM scores (D).)

(http://trnadb.bioinf.uni-leipzig.de/)
The tRNAdb, with one of the largest numbers of entries among RNA databases, is not only an excellent model system for implementing and validating algorithms and processes of automated nucleic acid data transfer, but also for the development of novel sequence analysis tools. It also provides a basis for integration of structurefunction relationships and additional information on evolution and phylogeny.

 http://trna.nagahama-i-bio.ac.jp/ This is the most accurate tRNA gene database curated manually by experts in the world This database is the outcome of the model project to utilize the expertise of elderly researchers and to pass it down to the next generation, which was carried out at Nagahama Institute of Bio-Science and Technology. Specifically, the existing multiple tRNA gene search programs are used for automatic search of tRNA gene from almost all sequenced prokaryote genomes, and then the experts manually check those cases in which different results are generated by program.

RDP-II(Ribosomal Database Project)

http://rdp.cme.msu.edu/ The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences. The ribosomal RNA sequences in the RDP-II alignments are mainly drawn from the major sequence repositories(Gen Bank, EMBL Data Library and DDBJ) According to RDP 10.28, it consists of 2,110,258 aligned and annotated 16S rRNA sequences.

TOOLS AVAILABLE

siRNAdb (http://sirna.sbc.su.se/)
The siRNA database provides a gene-centric view of human siRNA experimental data, including siRNAs of known efficacy and siRNAs predicted to be of high efficacy by siSearch The database contains information about siRNA molecules from two sources: (I) siRNAs collected from the literature that have experimentally verified efficacy and (ii) siRNAs selected computationally to target the REFSEQ curated human gene set

(http://www-snorna.biotoul.fr/)
snoRNA-LBME-db is a collection of human small nucleolar RNAs (snoRNAs) and Cajal body-specific RNAs (scaRNAs), that serve to guide modifications in rRNAs or snRNAs. The database can be search by sno/scaRNA name or Accession number, or by the position of the modified nucleotide in rRNA/snRNA sequence.

(http://www.arb-silva.de/)
SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya). SILVA are the official databases of the software package ARB.

This database is a comprehensive mammalian noncoding RNA database (RNAdb) containing sequences and annotations for tens of thousands of noncoding RNAs. These include a wide range of microRNAs, small nucleolar RNAs and larger mRNA-like ncRNAs. Some of these have documented functions and/or expression patterns, but the majority remains of unclear significance

The RNA modification database, RNAMDB

http://rna-mdb.cas.albany.edu/RNAmods/ The RNA modification database provides a comprehensive listing of post transcriptionally modified nucleosides from RNA . The RNAMDB provides a user-friendly, searchable interface that directs the user to a detailed information page for each database entry

RNA Sequence Database List

A list of RNA sequence databases are given in the following site. http://www.oxfordjournals.org/nar/database/cat/2 EXAMPLES: 16S and 23S Ribosomal RNA Mutation Database HuSiDa - Human siRNA database GtRDB - Genomic tRNA Database The Small Subunit rRNA Modification Database 3D rRNA modification maps siRNAdb

References
Nucleic Acids Research-OXOFORD journal
Rfam: an RNA family database, Nucleic Acids Research, 2003, Vol. 31, No. 1 439441,DOI: 10.1093/nar/gkg006 tRNAdb 2009: compilation of tRNA sequences and tRNA genes, Nucleic Acids Research, 2009, Vol. 37, Database issue D159 D162,doi:10.1093/nar/gkn772 Rfam: updates to the RNA families database, D136D140 Nucleic Acids Research, 2009, Vol. 37, Database issue, doi:10.1093/nar/gkn766