rna database

7/31/2019 RNA Database

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RNA DATABASES


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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 ofknown and predicted representative members of

the family, annotated with a consensus base-paired

secondary structure


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Seed alignment for the U12 spliceosomal RNA family.

Secondary structure base pairs are encoded in the coloured bases in the

alignment,


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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 thefraction of canonical base pairs (C) and CM scores (D).)


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(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 thedevelopment of novel sequence analysis tools.

It also provides a basis for integration of structure-

function relationships and additional information on

evolution and phylogeny.


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http://trna.nagahama-i-bio.ac.jp/

This is the most accurate tRNA gene databasecurated manually by experts in the world

This database is the outcome of the model projectto utilize the expertise of elderly researchers and topass it down to the next generation, which wascarried out at Nagahama Institute of Bio-Scienceand Technology. Specifically, the existing multiple

tRNA gene search programs are used for automaticsearch of tRNA gene from almost all sequencedprokaryote genomes, and then the expertsmanually check those cases in which different

results are generated by program.


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RDP-II(Ribosomal Database Project)

http://rdp.cme.msu.edu/

The Ribosomal Database Project (RDP) providesribosome related data services to the scientificcommunity, including online data analysis, rRNA

derived phylogenetic trees, and aligned andannotated rRNA sequences.

The ribosomal RNA sequences in the RDP-IIalignments are mainly drawn from the majorsequence 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.


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TOOLS AVAILABLE


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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


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(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.


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(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.


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This database is a comprehensive

mammalian noncoding RNA database

(RNAdb) containing sequences and

annotations for tens of thousands ofnoncoding RNAs.

These include a wide range of microRNAs,

small nucleolar RNAs and larger mRNA-like

ncRNAs. Some of these have documentedfunctions and/or expression patterns, but

the majority remains of unclear significance


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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 fromRNA .

The RNAMDB provides a user-friendly,

searchable interface that directs the user to

a detailed information page for each

database entry


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RNA Sequence Database List

A list of RNA sequence databases are given in thefollowing 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


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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

rna database

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