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1. Functional_RNAs
a. Non-Coding RNA database
http://biobases.ibch.poznan.pl/ncRNA/
Non-translatable RNA transcripts that appear to work at the RNA level.

b. Rfam
http://www.sanger.ac.uk/Software/Rfam/
Database of structure-annotated multiple sequence alignments, covariance models and family annotation for a number of non-coding RNA families

c. SCOR
http://scor.berkeley.edu/
The Structural Classification of RNA (SCOR) is a database designed to provide a comprehensive perspective and understanding of RNA motif structure, function, tertiary interactions and their relationships

d. tRNAscan-SE
http://www.genetics.wustl.edu/eddy/tRNAscan-SE/
tRNAscan-SE allows you to search for tRNA genes in genomic sequence. (site hosted by Eddy Lab at WashU)

2. RNA_General_Links_and_Information
a. NDB
http://ndbserver.rutgers.edu/
NDB (Nucleic Acid Database) is a repository of three-dimensional structural information about nucleic acids.

b. RNA folding Servers
http://kinefold.u-strasbg.fr/rna.html
List of RNA folding servers and related web sites maintained by Herve Isambert.

c. RNA Informatics Links
http://www-lbit.iro.umontreal.ca/RNA_Links/RNA.shtml
An exhaustive list of RNA links; from the experts in the Major lab.

d. RNAbase
http://www.rnabase.org/
RNAbase is a searchable and annotated database of all publicly available RNA structures.

e. The RNA World
http://www.imb-jena.de/RNA.html
An RNA resource hub.

f. The Zuker Group
http://www.bioinfo.rpi.edu/applications/mfold/
Algorithms, thermodynamics and databases for RNA secondary structure.

RNA_Motif_Search_and_Comparison
a. Riboswitch finder
http://riboswitch.bioapps.biozentrum.uni-wuerzburg.de/server.html
RNA motif search program that identifies RNA motifs called riboswitches which are metabolic binding domains in mRNA that regulate gene expression. The program was originally designed around a set of riboswitches found in Bacillus subtilis.

b. RNABOB
http://www.genetics.wustl.edu/eddy/software/#rnabob
Fast RNA motif/pattern searcher; from the authors: If you re looking for an RNA motif that fits a hard consensus pattern -- a la PROSITE patterns, but with base-pairing -- you might check out RNABOB; not a Web-tool; based on RNAMOT.

c. RNAMOT
http://www.esil.univ-mrs.fr/~dgaut/download/
RNA motif search program; not a Web-tool.

d. Transterm UTR Motif Search
http://guinevere.otago.ac.nz/transterm.html
Transterm is an interactive database providing access to RNA sequences and their associated motifs. The RNA sequences are derived from all gene sequence data in Genbank, including complete genomes, divided into putative 5' and 3'UTRs, initiation and term

e. http://www.ambion.com/techlib/
Company web site with very good technical resources including an excellent links page, summaries of recent papers on RNA-related topics, and free access to review articles and web features on RNA-related research topics.

3.RNA_Sequence_Retrieval
http://www.ncbi.nlm.nih.gov/
http://www.ebi.ac.uk/embl/index.html

1. BLAST
Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

2. EBI Tools
EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

3. EMBOSS
Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.

4. Entrez
NCBI information retrieval system, including GenBank, MMDB (structures), genomes, population sets, OMIM, taxonomy and PubMed.

5. FeatureExtract
The FeatureExtract server extracts sequence and feature annotations, such as intron/exon structure, from GenBank entries and other GenBank format files.

6. GeneLynx
A portal to the human genome. Query by text or BLAST, to access heaps of info from primary and secondary databases of genomic resources, transcripts, protein sequences, function, associated diseases, homologs, ests.

7. PubCrawler
It goes to the library. You go to the pub; receive email alerts for current contents of PubMed and GenBank; e.g. use accession number of htg record as query to receive sequence updates (as the version number changes).

8. Ribosomal Database Project
Highly curated database of aligned and annotated rRNA sequences with accompanying phylogenies; data available for download.

9. SeqHound
Seqhound is a sequence retrieval system that provides access to biological sequence, structure and functional annotation data. Seqhound can be accessed via the web interface, through the remote API, or by installing locally.

10. WU BLAST
Washington University Basic Local Alignment Search Tool

4.RNA_Structure_Predicition_and_Visualization
a. CARNAC
http://bioinfo.lifl.fr/carnac
Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned.

b. DEQOR
http://cluster-1.mpi-cbg.de/Deqor/deqor.html
Tool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene regions that have a high sil

c. ERPIN
http://tagc.univ-mrs.fr/erpin/
ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others

d. wustl
http://cic.cs.wustl.edu/RNA/
Server which provides iterated loop matching and maximum weighted matching algorithms for pseudoknot containing RNA secondary structure prediction. Algorithms can apply thermodynamic and comparative information, and thus can be used for either aligned

e. Kinefold
http://kinefold.u-strasbg.fr/
Kinefold calculates (and animates) the folding kinetics of RNA sequences including pseudoknots.

f. Mfold
http://www.bioinfo.rpi.edu/applications/mfold/old/rna/
Predict RNA secondary structure from sequence; does not predict pseudoknots

g.MolMovDB
http://molmovdb.org/
The Database of Macromolecular Movements (MolMovD contains a collection of animated protein and RNA structures to assist in the exploration of macromolecular flexibility. Software for structure analysis is also available.

h. MOLPROBITY
http://kinemage.biochem.duke.edu/molprobity/main.php?use_king=1
MOLPROBITY is a structure analysis and validation program that can calculate and display steric, H-bonding, and van der Waals interactions for known structures of proteins, nucleic acids, and complexes.

i. PKNOTS
http://www.genetics.wustl.edu/eddy/software/#pk
Predict pseudoknot structures in RNA sequence; source code on allowScriptAccess="never" allowNetworking="internal" wmode="transparent"ly.

j. RDfolder
http://rna.cbi.pku.edu.cn:1977/rna/index.php
A RNA secondary structure prediction program which implements two methods, on allowScriptAccess="never" allowNetworking="internal" wmode="transparent"e based on random stacking and the other based on helical region distributions.

f. RNAfold
http://www.tbi.univie.ac.at/cgi-bin/RNAfold.cgi
Predict RNA secondary structure from sequence; note sequence length limit.

g. RNAsoft
http://www.rnasoft.ca/
Software for RNA/DNA secondary structure prediction and design

h. Sfold
http://sfold.wadsworth.org
Server with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features.

i. siDirect
http://design.RNAi.jp/
Server for computing small interfering RNA (siRNA) sequences which are best suited for mammalian RNA interference (RNAi). The site accepts a sequence as input and returns a list of siRNA candidates.
j. siRNA Selection Server
http://jura.wi.mit.edu/bioc/siRNA
Server aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of the a potential siRNA.

k. siRNAdb
http://sirna.cgb.ki.se/
This resource includes siSearch, AOSearch, and a siRNAdb which provides a platform for mining an siRNA database, and searching for non-specific matches to your siRNA (small interfering RNAs).

l. siRNAdb
http://smi-web.stanford.edu/projects/helix/sstructview/
RNA secondary structure viewer applet; must be integrated into web page to be implemented; can link to multiple computational backends.

M.TROD
http://www.cellbio.unige.ch/RNAi.html
T7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase.It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering.

N.Vienna RNA Package
http://www.tbi.univie.ac.at/~ivo/RNA/
Comprises a C codelibrary and several stand-alone programs for the prediction and comparison of RNA secondary structures.

5. RNA: Three-Dimensional 3-D Structures
a. Ribosome Images (Wadsworth Center Microscope 3D Database)
http://www.wadsworth.org/spider_3d/home_page.html

b. RNase P 3D models
http://jwbrown.mbio.ncsu.edu/RNaseP/RNA/threeD/threeD.html
RNase P 3D models

c. SCOR: Structural Classification of RNA
http://scor.lbl.gov/
SCOR: Structural Classification of RNA

d. The Nucleic Acid Database (ND
http://ndbserver.rutgers.edu/NDB/

6.UTR bioinformatics
a.UTR Blast
http://www.ba.itb.cnr.it/BIG/Blast/BlastUTR.html
UTRBlast is an on allowScriptAccess="never" allowNetworking="internal" wmode="transparent"line tool which can blast your untranslated region UTR and compare its similarity to other UTR regions.

b.UTR Home
http://www.ba.itb.cnr.it/BIG/UTRHome/
UTR Home. A collection of UTR resources and on allowScriptAccess="never" allowNetworking="internal" wmode="transparent"line tools.

c. UTRdb
http://www.ba.itb.cnr.it/srs7bin/cgi-bin/wgetz?-page+top
UTRdb. A database of UTR sequences. Find your UTR RNA or DNA sequence of interest.

d. UTRScan UTR Scan
http://www.ba.itb.cnr.it/BIG/UTRScan/
UTRScan UTR Scan.The program UTRscan looks for UTR functional elements by searching through user submitted sequence data for the patterns defined in the UTRsite collection.

e. UTRSite
http://www2.ba.itb.cnr.it/UTRSite/
UTRSite is a collection of functional sequence patterns located in 5' or 3' UTR sequences.