Motifs

Included are RNA motif search programs to help analyze recurrent subsets of nucleotide arrangements in secondary or tertiary structure.

Found 25 links

Displaying 15 links

ERPINTool Content

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

Freiburg RNA ToolsTool Content

http://rna.informatik.uni-freiburg.de

The Freiburg RNA Tools web server contains tools for the advanced analysis of RNA. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA-RNA interaction, exact RNA matching and alignment of RNA, respectively.

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

ITS2Tool Content

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

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.

MicroInspectorTool Content

http://bioinfo.uni-plovdiv.bg/microinspector/

MicroInspector is a tool that detects miRNA (microRNA) binding sites in your input sequence by searching against databases of known miRNA binding sites.

MoD ToolsTool Content

http://159.149.109.16/modtools/

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.

PatMatchTool Content

http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl

PatMatch is a pattern matching tool that allows you to search for short (<20 residues) nucleotide or peptide sequences and can accomodate ambiguous/degenerate patterns.

PREP SuiteTool Content

http://prep.unl.edu/

The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included.

This content is being maintained by jpmower.

QGRS MapperTool Content

http://bioinformatics.ramapo.edu/QGRS/index.php

Quadruplex forming G-Rich Sequences (QGRS) Mapper searches nucleotide sequences for the presence of G-quartet motifs. QGRS Mapper allows you to view the distribution and composition of QGRS in the context of alternatively spliced isoforms of your gene.

RADARTool Content

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

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.

RegRNATool Content

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

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.

Tags associated with subcategory 'RNA/Motifs'

rna sequence analysis nucleic acid conformation rna sequence alignment algorithms computational biology dna sequence analysis conserved sequence nucleic acid sequence homology ribonucleic acid regulatory sequences base sequence binding sites dna humans untranslated rna messenger rna molecular sequence data eukaryotic cells biomedical engineering factual databases evaluation studies as topic chemical dictionaries automated pattern recognition bacterial genome molecular structure nucleic acids macromolecular substances likelihood functions calcium calcium-binding proteins protein conformation reproducibility of results archaeal genome bacterial genes archaeal genes anti-infective agents plant dna micrornas ribosomal rna gene expression regulation protein sequence analysis protein databases probability open reading frames peptides proteins proteome viral genome allosteric regulation ubiquitin secondary protein structure sequence analysis statistical models molecular models transfer rna sensitivity and specificity selenocysteine iron response elements gene expression genetic databases leghemoglobin initiator codon histones genome genomics transcriptional regulatory elements yeasts animals base pairing amino acid sequence homology amino acid sequence arabidopsis proteins amino acid motifs plant proteins protein binding x-ray crystallography rna editing structure-activity relationship forecasting iron-regulatory proteins biomolecular nuclear magnetic resonance arabidopsis bayes theorem cytidine mitochondrial genes chloroplasts chloroplast rna eukaryota fungi mitochondrial proteins plant gene expression regulation consensus sequence 5' flanking region catalytic rna chemical models plant genes genetic markers programming languages computer simulation genetic promoter regions