>
Tag
> Links tagged with 'transfer rna'

Links tagged with 'transfer rna'

RSS FeedCompact ViewList as XMLList as JSON

Found 14 links

Displaying 14 links

BROPResource Content

http://brop.org/

Expression > Transcript Expression Analysis
Model Organisms > Microbes

The Bioinformatics Resource for Oral Pathogens (BROP) contains tools for genomics of oral pathogens including Genome Viewer, GOAL (genome wide ORF alignment), an oral pathogen microarray database, an entrez counter, oral pathogen specific BLAST, and a codon usage database.

NAR Web Server Issue 2005
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsbacteria bacterial capsules bacterial genes bacterial genome bacterial polysaccharides bacterial proteins biological evolution computational biology dna transposable elements fungal genome genetic databases genetic variation genomic islands genomics horizontal gene transfer integrases mouth oligonucleotide array sequence analysis open reading frames operon porphyromonas gingivalis sequence alignment streptococcus mutans transfer rna virulence virulence factors

CentroidFoldTool Content

http://www.ncrna.org/centroidfold/

RNA > Structure Prediction, Visualization, and Design

Recognizing the growing role for non-coding RNAs (ncRNAs) in cells, the CentroidFold web server predicts RNA secondary structure from input sequence data (single or multiple alignments).

NAR Web Server Issue 2009
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms nucleic acid conformation rna sequence analysis sequence alignment transfer rna untranslated rna

CLIPZDatabase Content

http://www.clipz.unibas.ch

RNA > Databases

CLIPZ supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other type of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The CLIPZ platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets.

This content is being maintained by nonb@nih.gov.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals binding sites genetic databases genome humans messenger rna mice rna sequence analysis rna-binding proteins transfer rna untranslated 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
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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

ILMTool Content

http://cic.cs.wustl.edu/RNA/

RNA > Structure Prediction, Visualization, and Design

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 or individual sequences.

NAR Web Server Issue 2004
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms bacillus subtilis bacterial rna base composition base pairing base sequence escherichia coli feedback molecular models molecular sequence data nucleic acid conformation nucleic acid sequence homology phylogeny reproducibility of results rna rna sequence analysis sensitivity and specificity sequence alignment theoretical models thermodynamics transfer rna

MobilomeFINDERTool Content

http://mml.sjtu.edu.cn/MobilomeFINDER/

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MobilomeFINDER (Mobile Genome FINDER) is a tool for high-throughput genomic island discovery.

NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms bacterial genes bacterial genome bacterial rna computational biology enterobacteriaceae escherichia coli escherichia coli k12 fungal gene expression regulation genomic islands genomics oligonucleotide array sequence analysis polymerase chain reaction pseudomonas aeruginosa shigella shigella flexneri streptococcus suis theoretical models transfer rna

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
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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

R3D-BLASTTool Content

http://genome.cs.nthu.edu.tw/R3D-BLAST/

RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Similarity Searching

R3D-BLAST is a BLAST-like search tool that allows users to quickly search against the PDB for RNA structures sharing similar substructures with a specified query RNA structure. Input is an RNA 3D structure in PDB format; output includes a graphical display showing structural superposition.

This content is being maintained by cllu.

NAR Web Server Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms nucleic acid conformation protein databases rna transfer rna

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
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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

TFAMTool Content

http://tfam.lcb.uu.se/

RNA > Functional RNAs

TFAM is a system to classify the function of tRNAs that is based on tRNA structural alignments.

NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalphaproteobacteria animals bacterial dna bacterial genome computational biology drosophila melanogaster genetic variation genomics histidine-trna ligase horizontal gene transfer molecular evolution nucleic acid databases phylogeny statistical models transfer rna

tRNADB-CEDatabase Content

http://trna.nagahama-i-bio.ac.jp

RNA > Databases

The tRNA Gene DataBase Curated by Experts "tRNADB-CE" contains tRNA sequences.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsdna sequence analysis genes genomics metagenomics nucleic acid databases phylogeny transfer rna

tRNAscan-SETool Content

http://lowelab.ucsc.edu/tRNAscan-SE/

RNA > Functional RNAs

tRNAscan-SE allows you to search for tRNA genes in genomic sequence. (site hosted by Lowe Lab at UCSC)

NAR Web Server Issue 2005
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals bacterial rna evaluation studies as topic factual databases genome genomics introns rna small nucleolar rna transfer rna