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Links tagged with 'ribonucleic acid regulatory sequences'

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ERPINTool Content

http://tagc.univ-mrs.fr/erpin/

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

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) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.

NAR Web Server Issue 2004
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tagsalgorithms base sequence computational biology conserved sequence gene expression regulation iron nucleic acid conformation nucleic acid sequence homology response elements ribonucleic acid regulatory sequences ribosomal rna rna rna sequence analysis selenocysteine sensitivity and specificity sequence alignment transfer rna

MoD ToolsTool Content

http://159.149.109.16/modtools/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs

Tools for Motif Discovery (MoD) in nucleotide sequences that includes: Weeder, a program for detecting transcription factor binding sites (TFBS) in coregulated genes; WeederH, a tool for detecting TFBS and regulatory regions from homologous genes; and RNA profile, a tool for secondary structure motif discovery in RNA sequences.

NAR Web Server Issue 2006
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tagsbinding sites dna sequence analysis gene expression regulation nucleic acid conformation nucleic acid sequence homology ribonucleic acid regulatory sequences rna sequence analysis transcription factors transcriptional regulatory elements untranslated rna

RADARTool Content

http://datalab.njit.edu/biodata/rna/RSmatch/server.htm

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

RADAR (RNA Data Analysis and Research) provides multiple tools for RNA structure analysis including: pairwise structure alignment, multiple structure alignment, constrained structure alignment, database searching, and prediction of the consensus structure for a set of RNA sequences.

NAR Web Server Issue 2007
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tagsalgorithms base sequence computational biology computer simulation conserved sequence genetic databases humans molecular sequence data nucleic acid conformation nucleic acid sequence homology ribonucleic acid regulatory sequences rna rna sequence analysis sequence alignment untranslated rna

RegRNATool Content

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

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Splicing
RNA > Functional RNAs
RNA > Motifs

Regulatory RNA (RegRNA) is a server for identifying regulatory RNA motifs and elements in mRNA sequences including: motifs located in the 5\'-UTR and 3\'-UTR; motifs involved in mRNA splicing and transcriptional regulation; other motifs in mRNA such as riboswitches and splice donor/acceptor sites; RNA structural features; and miRNA target sites.

NAR Web Server Issue 2006
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tagsanimals humans messenger rna mice nucleic acid conformation nucleic acid sequence homology rats ribonucleic acid regulatory sequences rna sequence analysis systems integration untranslated regions

Rescue-ESETool Content

http://genes.mit.edu/burgelab/rescue-ese/

DNA > Structure and Sequence Feature Detection
Expression > Splicing

Server for the identification of hexnucleotide exonic splicing enhancers (ESEs). Also contains a list of 238 identified ESEs for human genes.

NAR Web Server Issue 2004
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tagsanimals complementary dna computational biology consensus sequence dna sequence analysis exons genes human genome humans hypoxanthine phosphoribosyltransferase introns messenger rna mice nucleic acid databases nucleic acid regulatory sequences oligonucleotides point mutation ribonucleic acid regulatory sequences rna precursors rna sequence analysis rna splicing tetraodontiformes zebrafish

RibExTool Content

http://www.ibt.unam.mx/biocomputo/RibEx.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Riboswitch Explorer (RibEx) searches sequences for known riboswitches and also for predicted bacterial regulatory elements that are highly conserved

NAR Web Server Issue 2005
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tagsbacterial gene expression regulation bacterial rna base sequence conserved sequence dna sequence analysis open reading frames ribonucleic acid regulatory sequences

Riboswitch finderTool Content

http://riboswitch.bioapps.biozentrum.uni-wuerzburg.de/server.html

Expression > Gene Regulation
RNA > Motifs

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.

NAR Web Server Issue 2004
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tagsallosteric regulation messenger rna nucleic acid conformation ribonucleic acid regulatory sequences rna sequence analysis

RNA AnalyzerTool Content

http://rnaanalyzer.bioapps.biozentrum.uni-wuerzburg.de/

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

RNA Analyzer searches for known structures and identifies RNA motifs in your input sequence.

NAR Web Server Issue 2003
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tagscatalytic rna messenger rna nucleic acid conformation ribonucleic acid regulatory sequences rna sequence analysis

RNAborTool Content

http://bioinformatics.bc.edu/clotelab/RNAbor/

RNA > Structure Prediction, Visualization, and Design

RNAbor is a server for computing structural neighbors of a RNA secondary structure.

NAR Web Server Issue 2007
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tagscluster analysis computational biology computer simulation conserved sequence genetic databases molecular sequence data nucleic acid conformation nucleic acid sequence homology ribonucleic acid regulatory sequences rna rna sequence analysis sequence alignment untranslated rna

RNALogoTool Content

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

RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Multiple Sequence Alignments

RNALogo is a tool for graphical representation of features within multiple RNA sequence alignments and their consensus RNA secondary structures. Each RNA family in Rfam has been graphically evaluated for a logo.

NAR Web Server Issue 2008
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tagsnucleic acid conformation ribonucleic acid regulatory sequences rna rna sequence analysis sequence alignment

RNAzTool Content

http://rna.tbi.univie.ac.at/cgi-bin/RNAz.cgi

RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Analysis of Aligned Sequences

RNAz detects functional RNA secondary structures in multiple sequence alignments based on thermodynamic stability and structural conservation.

NAR Web Server Issue 2007
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tagsalgorithms archaea base sequence computational biology consensus sequence conserved sequence escherichia coli genome molecular evolution molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology phylogeny prokaryotic cells ribonucleic acid regulatory sequences ribosomal rna rna rna sequence analysis rna stability sequence alignment thermodynamics untranslated rna

SIREsTool Content

http://ccbg.imppc.org/sires/index.html

Expression > Gene Regulation
RNA > Motifs

SIREs is an iron responsive element prediction tool. From input data, SIREs produces structure analysis, predicted RNA folds, folding energy data and overall quality flags.

NAR Web Server Issue 2010
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tagsalgorithms binding sites humans iron iron-regulatory proteins nucleic acid conformation ribonucleic acid regulatory sequences rna untranslated regions

SROOGLETool Content

http://sroogle.tau.ac.il

Expression > Splicing

SROOGLE is a webserver that makes splicing signal sequence and scoring data available to the biologist in an integrated, visual and user friendly format.

NAR Web Server Issue 2009
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tagsexons introns ribonucleic acid regulatory sequences rna splice sites rna splicing systems integration