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NRED

http://research.imb.uq.edu.au/NRED

Description :
Noncoding RNA Expression Database

piRNABank

http://pirnabank.ibab.ac.in/

Description :
Sequences and properties of Piwi-interacting RNAs (piRNAs) in human, mouse and rat

sRNAMap

http://srnamap.mbc.nctu.edu.tw/

Description :
small regulatory RNA in microbial genomes

R-Coffee

http://www.tcoffee.org/

Description :
The R-Coffee web server uses pairwise or multiple sequence alignment methods to produce multiple alignments of non-coding RNA sequences, incorporating predicted or known secondary structures.

Software.ncrna.org

http://software.ncrna.org/

Description :
A suite of tools for analyzing non-coding RNA sequences on the basis of their secondary structures. Tools include those for structural multiple sequence alignments, structural pairwise sequence alignments and structural motif finding.

WAR

http://genome.ku.dk/resources/war

Description :
Webserver for Aligning structural RNAs (WAR) is a collection of methods for performing multiple alignments and secondary structure prediction for non-coding RNA sequences. The methods can be run simultaneously and a consensus prediction calculated.

Non-Coding RNA database

http://biobases.ibch.poznan.pl/ncRNA/

Description :
Non-translatable RNA transcripts that appear to work at the RNA level.

Rfam

http://www.sanger.ac.uk/Software/Rfam/

Description :
Database of structure-annotated multiple sequence alignments, covariance models and family annotation for a number of non-coding RNA families.

NONCODE

http://www.bioinfo.org.cn/NONCODE/index.htm

Description :
A database of noncoding RNAs

fRNAdb

http://www.ncrna.org/

Description :
Functional RNA Database (fRNAdb) is a database service that hosts a large collection of non-coding transcripts including annotated/un-annotated sequences from H-inv database, NONCODE, and RNAdb. A set of computational sequence analyses are performed over these registered sequences. The analyses include RNA secondary structure motif discovery, EST support, finding cis-regulatory elements, sequence homology search, etc. The fRNAdb provides an efficient interface to help users filter out particular transcripts that match their own criteria to sort out functional RNA candidates.

Guide RNA Database

http://biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html Guide RNA sequences

HyPaLib

http://bibiserv.techfak.uni-bielefeld.de/HyPa/ The database, called HyPaLib (for Hybrid Pattern Library), contains annotated structural elements characteristic for certain classes of structural and/or functional RNAs. These elements are described in a language specifically designed for this purpose. The language allows to conveniently specify hybrid patterns, i.e. motifs consisting of sequence features and structural elements together with sequence similarity and thermodynamic constraints. We are currently developing software tools that allow a user to search sequence databases for any pattern in HyPaLib, thus providing functionality which is similar to PROSITE, but dedicated to the more complex patterns in RNA sequences. HyPaLib is available at http://bibiserv.techfak.uni- bielefeld.de/HyPa/.

IRESdb - the Internal Ribosome Entry Site database

http://ifr31w3.toulouse.inserm.fr/IRESdatabase/

Description :
Internal Ribosome Entry Sites (IRES) are cis-acting RNA sequences able to mediate internal entry of the 40S ribosomal subunit on some eukaryotic and viral messenger RNAs upstream of a translation initiation codon. These sequences are very diverse and are present in a growing list of mRNAs. Novel IRES sequences continue to be added to public databases every year and the list of unknown IRESes is certainly still very large. The IRES database is a comprehensive WWW ressource for internal ribosome entry sites and presents currently available general informations as well as detailed data for each IRES. It is a searchable, periodically updated collection of IRES RNA sequences. Sequences are presented in FASTA form and hotlinked to NCBI GenBank files. Several subsets of data are classified according to the viral taxon (for viral IRESes), to the gene product function (for cellular IRESes), to the possible cellular regulation or to the trans-acting factor that mediates IRES function. This database is accessible at http://ifr31w3.toulouse.inserm.fr/IRESdatabase/.

MODOMICS

http://genesilico.pl/modomics/

Description :
MODOMICS (‘omics’ approach to RNA modification) integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that carry out the respective reactions. MODOMICS also provides literature information, and links to other databases, including the available protein sequence and structure data. MODOMICS can be queried by the type of nucleoside (e.g. A, G, C, U, I, m1A, nm5s2U etc.), type of RNA, position of a particular nucleoside, type of reaction (e.g. methylation, thiolation, deamination, etc.), and name or sequence of an enzyme of interest. Options for data presentation include graphs of pathways involving the query nucleoside, multiple sequence alignments of RNA sequences and tabular forms with enzyme and literature data. The contents of MODOMICS can be accessed through the World Wide Web at http://genesilico.pl/modomics/.

Recent develoments :
The current list of modifications and pathways is comprehensive. The dataset of enzymes is limited to Escherichia coli and Saccharomyces cerevisiae and sequence alignments (and localization of modified nucleosides) are available only for tRNAs from these organisms. tRNAs and enzymes from other organisms as well as other RNAs will be included in the near future.

Aknowledgement :
MODOMICS would not be possible without the data from publicly available databases, in particular the RNAMods database and the Bayreuth tRNA dataset. We are grateful to Daylight Chemical Information Systems Inc. for providing their SMI2GIF service. Our work is supported by the EMBO/HHMI Young Investigator Programme award to J.M.B. S.D.H. was supported by the NIH (grant 5R01AI056034-02). Travel expenses between Poland and France were covered by EGIDE (Polonium grant #07558WK) and by the CEMBM Center of Excellence grant from the 5th Framework Programme of the European Union (contract #QLK6-CT-2002-90363).

References :
1. Bujnicki J.M., Droogmans L., Grosjean H., Purushothaman S.K., Lapeyre B. (2004) Bioinformatics-guided identification and experimental characterization of novel RNA methyltransferases. In Nucleic Acids and Molecular Biology series, "Practical Bioinformatics". Editor: Bujnicki JM. Springer-Verlag.
2. Dunin-Horkawicz S., Czerwoniec A., Gajda M.J., Feder M., Grosjean H., Bujnicki J.M. (2006) MODOMICS: a database of RNA modification pathways. Nucleic Acids Res Database Issue (in press).

ncRNAs database

http://biobases.ibch.poznan.pl/ncRNA/

Description :
The noncoding RNAs database is a colection of currently available sequence data on RNAs, which do not have protein-coding capacity and have been implicated in regulation of cellular processes. The RNAs included in the database form very heterogenous group of molecules that cat on different levels of information transmission in the cell. It includes RNAs acting on the level of chromatin structure, throug transcriptional and translational regulation of gene expression to modulation of protein function and regulation of subcellular distribution of RNAs and proteins. Some of these RNAs have been shown to be connected with developmental disorders in humans. In recent years RNAs with potential regulatory functions have been found in prokaryotic, animal and plant cells. Currently the database contains over 100 sequences of noncoding RNAs and can be accessed via WWW at http://biobases.ibch.poznan.pl/ncRNA/ .

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