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Links tagged with 'ribosomal rna'

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Found 15 links

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CARNACTool Content

http://bioinfo.lifl.fr/carnac

RNA > Structure Prediction, Visualization, and Design

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.

NAR Web Server Issue 2004
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tagsalgorithms catalytic rna cytochromes endoribonucleases enterovirus genetic models messenger rna molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology ribonuclease p ribosomal rna rna rna sequence analysis sequence alignment statistical models telomerase viral rna

CorreLogoTool Content

http://correlogo.abcc.ncifcrf.gov/

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

CorreLogo generates a 3D sequence logo for RNA or DNA alignments. The first two dimensions of the sequence logo display information about the information content and residue composition of individual columns of the alignment. The 3D sequence logo consists of a square matrix that shows columns with high mutual information, a measure of how much the residues in two alignment columns are correlated.

NAR Web Server Issue 2006
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tagsdna sequence analysis nucleic acid conformation ribosomal rna rna sequence analysis sequence alignment transfer rna

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

ITS2Tool Content

http://its2.bioapps.biozentrum.uni-wuerzburg.de/

DNA > Phylogeny Reconstruction
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre-calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy.

NAR Web Server Issue 2006
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tagsanimals base sequence computational biology conserved sequence eukaryota fungal genome fungi genetic databases genetic markers genetic transcription invertebrates molecular evolution molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology phylogeny plant genome plants ribosomal rna ribosomal spacer dna rna sequence analysis sequence alignment tertiary protein structure

NASTTool Content

http://greengenes.lbl.gov/cgi-bin/nph-NAST_align.cgi

DNA > Phylogeny Reconstruction
Model Organisms > Microbes
RNA > General Resources
Sequence Comparison > Multiple Sequence Alignments

Nearest Alignment Space Termination (NAST) is a multiple sequence alignment server for comparative analysis of 16S rRNA gene sequences from bacteria and archaea.

NAR Web Server Issue 2006
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tagsalgorithms archaeal genes bacillus anthracis bacterial genes cluster analysis computer-aided design dna probes dna sequence analysis equipment design gene expression profiling nucleic acid sequence homology oligonucleotide array sequence analysis ribosomal rna rrna genes sequence alignment staphylococcus aureus

NDB ToolsTool Content

http://ndbserver.rutgers.edu/services/

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

The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures.

NAR Web Server Issue 2003
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tagsalgorithms base pairing base sequence chemical models dna factual databases molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology proteins restriction mapping ribosomal rna rna signal recognition particle statistical data interpretation stereoisomerism terminology as topic water

POPSTool Content

http://mathbio.nimr.mrc.ac.uk/wiki/POPS

Protein > 3-D Structural Features

Parameter OPtimised Surfaces (POPS) is an algorithm to calculate accessible surfaces areas at atomic and residue level.

NAR Web Server Issue 2003
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tagsalgorithms amino acids hydrophobic and hydrophilic interactions macromolecular substances molecular models molecular structure nucleic acid conformation nucleic acids protein binding protein conformation proteins ribosomal proteins ribosomal rna ribosomes solvents time factors transfer rna

REPKTool Content

http://rocaplab.ocean.washington.edu/tools/repk

DNA > Tools For the Bench
Model Organisms > Microbes

REPK (Restriction Endonuclease Picker) assists in the choice of restriction endonucleases for terminal restriction fragment length polymorphism (T-RFLP) by finding sets of four restriction endonucleases which together uniquely differentiate user-designated sequence groups.

NAR Web Server Issue 2007
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tagsalgorithms bacteria bacterial dna computational biology ecosystem enzymes factual databases microbiology phylogeny restriction fragment length polymorphism ribosomal dna ribosomal rna

Ribosomal Database ProjectDatabase Content

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

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
RNA > Functional RNAs
RNA > Sequence Retrieval

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

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tagsanimals archaea archaeal rna bacteria bacterial rna eukaryotic cells nucleic acid databases phylogeny prokaryotic cells ribosomal 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

SeaviewTool Content

http://pbil.univ-lyon1.fr/software/seaview.html

Sequence Comparison > Alignment Editing and Visualization

SeaView is a graphical multiple sequence alignment editor that is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW programs to locally improve the alignment.

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tagsanimals base sequence dna molecular evolution molecular sequence data phylogeny proteins ribosomal rna sequence alignment

SfoldTool Content

http://sfold.wadsworth.org

DNA > Tools For the Bench
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design

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.

NAR Web Server Issue 2004
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tagsalgorithms animals antisense oligonucleotides antisense rna base sequence bayes theorem binding sites catalytic rna computational biology drug design escherichia coli molecular sequence data nucleic acid conformation phylogeny probability protozoan rna rabbits ribosomal rna rna rna stability small interfering rna spliced leader rna statistical distributions statistical models tetrahymena thermophila thermodynamics transfer rna xenopus laevis

snoGPSTool Content

http://lowelab.ucsc.edu/snoGPS/

RNA > Functional RNAs

snoGPS allows you to search for H/ACA snoRNA (small nucleolar RNA) genes in a genomic sequence

NAR Web Server Issue 2005
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tagsalgorithms base sequence computational biology fungal genome fungal rna genomics guide rna molecular sequence data phylogeny pseudouridine ribosomal rna saccharomyces cerevisiae small nucleolar rna transfer rna

snoscanTool Content

http://lowelab.ucsc.edu/snoscan/

RNA > Functional RNAs

Snoscan allows you to search for C/D box methylation guide snoRNA (small nucleolar RNA) genes in a genomic sequence

NAR Web Server Issue 2005
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tagsalgorithms base pairing cell nucleolus fungal rna genetic models methylation ribose ribosomal rna saccharomyces cerevisiae small nuclear rna statistical models

SSATool Content

http://www.isrec.isb-sib.ch/ssa/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Signal Search Analysis (SSA) allows for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site (e.g. a transcription start site).

NAR Web Server Issue 2003
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tagsbacterial genome consensus sequence dna sequence analysis genetic promoter regions nucleic acid regulatory sequences protein biosynthesis response elements ribosomal rna transcription initiation site