Bioinformatics & Genomics
Companies, Publishers, & Books
Compendiums & Lists of Resource Links
Compounds & Enzymes
Educational & Information Resources
Genomics & DNA Sequence Analysis
Hidden Markov Models
Major Sites & Organizations
Metabolic Pathway Databases & Related
Molecular Modeling & Visualization
Motif, Domain, Profile, Pattern, & Repeat Searches
Multiple Alignment & Phylogeny
Protein & Nucleic Acid Search Servers
Protein Analysis from Sequence
Sites with Multiple or Integrated Tools
Software Catalogues, Lists, & Downloads
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Comparative RNA Web Site
[University of Texas] A comprehensive site with information on RNA including methods in structure prediction, RNA sequence/structure database, RNA structure information, RNA structure analysis, and rRNA structure-based phylogeny.
Computational Molecular Biology
[Washington Univ. at St. Louis] Topics covered include sequence alignment algorithms, multiple sequence alignment, RNA structure prediction, motif and pattern searches, and phylogenetic inference.
HTDB: Human Transcript Database
[Human Genome Sequencing Center, Baylor College of Medicine] A curated source for information related to RNA molecules that have been sequenced. The goal of HTD is to provide a clone-based platform that represents as many of the human transcripts that have been sequenced as possible.
LSU rRNA database
[Departement Biochemie, Universiteit Antwerpen] A database on the structure of large ribosomal subunit RNA including indications of secondary structure elements for each sequence.
[University of Montreal] This program determines 3D protein and RNA structures.
[TIGR] RBSfinder is a
Perl script that
algorithm to find ribosome binding
sites for genes in bacterial and
archaeal genomes. It is normally run as
a post-processor to the Glimmer gene
finder or to other prokaryotic gene
Ribosomal Database Project II
[Center for Microbial Ecology] The Ribosomal Database Project (RDP) compiles ribosomal sequences and related data and redistributes them in aligned and phylogenetically ordered form. These sequences are drawn from various rRNA collections such as GenBank and from individual laboratories around the world. The database contains over 3000 aligned small subunit (SSU) and large subunit (LSU) ribosomal RNA sequences. Prokaryotic sequences predominate.
RNA MFold Server
[Washington Univ. Medical School] RNA folding prediction by energy minimization.
RNA Modification Database
[Univ. of Utah] A comprehensive list of post-transcriptionally modified nucleotides from RNA.
RNA Structure Logo
[Technical University of Denmark] This server displays the information contents of structural RNA alignments as "structure logos." These graphically show the sequence information, as well as gaps and mutual information of base paired positions.
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The RNA World Website
[IMB-JENA] An extensive list of links to RNA related databases and web tools.
[CABIOS] An application that uses RNA optimal structure, basepair-probability matrix, and heat curve calculation to predict RNA structure.
The rRNA WWW Server
[Univ. of Antwerp, Belgium] Links to the LSU rRNA Database (aligned sequences from the large subunit rRNA); the SSU rRNA Database (aligned sequences from the small subunit rRNA); DCSE (multiple sequence alignment editor) Home Page; TREECON (tree construction); and TRAFOR (format conversion).
SRPDB: Signal Recognition Particle Database
[Univ of Texas Health Center] Provides annotated SRP RNA sequences from eukaryotes and archaea, phylogenetically ordered and aligned with their bacterial equivalents. We also make available representative RNA secondary structure diagrams where each base pair is proven by comparative sequence analysis.
SSU rRNA database
[Departement Biochemie, Universiteit Antwerpen] A database on the structure of small ribosomal subunit RNA including indications of secondary structure elements for each sequence.
tmRDB: tmRNA Database
[University of Texas Health Center] A database on the structures and functions of the tmRNA (earlier called "10S RNA"). The database provides aligned, annotated and phylogenetically ordered tmRNA sequences. The alignments of the sequences represent conserved secondary structure elements.
Vienna RNA Package
[Institut für theoretische Chemie] A package for RNA secondary structure prediction and comparison consisting of a code library and several stand-alone programs for prediction and comparison.