> Tag > Links tagged with 'ribosomal rna'

Links tagged with 'ribosomal rna'

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ERPINTool Content

http://tagc.univ-mrs.fr/erpin/ [open in a new window]

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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.

links directory index: 165
TitlePublication YearGoogle Scholar Citation Count
The ERPIN server: an interface to profile-based RNA motif identification200436
Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles2001129
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/ [open in a new window]

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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.

links directory index: 276
TitlePublication YearGoogle Scholar Citation Count
The ITS2 Database III--sequences and structures for phylogeny201038
The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses200667
Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures200559
A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota2005112
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 [open in a new window]

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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.

links directory index: 471
TitlePublication YearGoogle Scholar Citation Count
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes2006398
Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA200373
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/ [open in a new window]

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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.

links directory index: 1276
TitlePublication YearGoogle Scholar Citation Count
Tools for the automatic identification and classification of RNA base pairs2003125
Geometric nomenclature and classification of RNA base pairs2001373
The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids1992778
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 [open in a new window]

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Protein > 3-D Structural Features

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

links directory index: 114
TitlePublication YearGoogle Scholar Citation Count
POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level200349
Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome200265
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

Ribosomal Database ProjectDatabase Content

http://rdp.cme.msu.edu/ [open in a new window]

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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.

links directory index: 1063
TitlePublication YearGoogle Scholar Citation Count
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy20031063
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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

SfoldTool Content

http://sfold.wadsworth.org [open in a new window]

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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.

links directory index: 637
TitlePublication YearGoogle Scholar Citation Count
Sfold web server for statistical folding and rational design of nucleic acids2004221
A statistical sampling algorithm for RNA secondary structure prediction2003243
Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond2001125
A bayesian statistical algorithm for RNA secondary structure prediction199948
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/ [open in a new window]

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RNA > Functional RNAs

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

links directory index: 224
TitlePublication YearGoogle Scholar Citation Count
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs2005125
Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome200499
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/ [open in a new window]

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RNA > Functional RNAs

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

links directory index: 360
TitlePublication YearGoogle Scholar Citation Count
A computational screen for methylation guide snoRNAs in yeast1999360
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

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