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【共享】【转载】RNA informatics
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RNA informatics http://www-lbit.iro.umontreal.ca/RNA_Links/RNA.shtmlStereo view of the leadzyme complex with lead. -------------------------------------------------------------------------------- The past decade has been important for RNA molecules.The discovery of RNA catalytic properties by Cech, Guerrier-Takada and colleagues in 1983 has greatly intensified research activities on RNA function. On the other hand, RNA informatics has not been developed accordingly, and a huge amount of RNA data is waiting to be processed and analyzed. There is currently a need for new software tools to search for functional RNAs, to compute RNA sequence alignments, and to predict RNA secondary and 3-D structures. We collected here RNA database and tool links. -------------------------------------------------------------------------------- Databases Sequence GenBank NCBI EMBL Genome Sequencing Center The Sanger Centre Genome Database gdb Bacillus subtilis Genome sequencing projet Main centers for genomics Genome sequencing projets Con A-Sctivates chicken T cell EST database GOBASE DATABANKS TIGR RNA mods 5S ribosomal RNA Ribosomal RNA Mutational Database tRNA yeast Saccharomyces cerevisiaedatabase Non-coding RNA Database snoRNA Database snoRNA Database for Saccharomyces cerevisiae RNA Aptamer Sequence Database Fetch get sequences Kinetoplast Minicircle Sequence Database GenomeNet Sequences similarity search BLAST FASTA Aligned Sequences tRNA Steinberg alignment SSu and LSU rRna ANTWERP CAMUS Compressed database for homology searches AND MUltiple-aligned Sequence database Secondary Structure 16S and 23S and Group I Intron rRNA Secondary Structures Viroid, Viroid-like RNA Database PseudoBase RNA pseudoknots database Three-dimensional Structure Brookhaven National Laboratory PDB Nucleic Acid Database Others BPdatabase Base pairing classification The DEAMBULUM Information center Non-Canonical Base Pair Database MOTIF Searching Protein and Nucleic Acid Sequence Motifs MAGPIE Genome Analysis and Annotation MBGD Microbial Genome Database for Comparative Analysis ARCHAIC Archebacterial Information Collection RNase P, Westhof RNase P, Ribonuclease P Sequence Database SRPDB and uRNADB Uridine Insertion/Deletion Edited Sequence Database tmRNA RDP Ribosomal Database Project Riboweb -------------------------------------------------------------------------------- Sequence Sequences analysis UCS Sequence Alignment Package EMBOSS sequence analysis package -------------------------------------------------------------------------------- Multiple Sequence Alignment Pairwise Comparaison DCSE ClustalW-1.6 multiple alignment program Statistical and Learning Methods SAM Sequence Alignment and Modeling System RNASA Multiple RNA-Sequence alignment considering stem regions HMMER Others GCG Sequence Analysis Software Package Demo Version 1.3 BOXSHADE 3.21 Pretty Printing and Shading of Multiple-Alignment files GENIO/logo Calculation and display of positional dependent information content of nucleotide and amino acid sequences -------------------------------------------------------------------------------- Predicting Secondary Structure Genetic Algorithm Star Structure Analysis of Rna RNAGA Prediction of common secondary structures of RNAs Dynamic Programming Single Sequence mFold PKNOTS RNA folding including RNA pseudoknots. RNAfold Vienna package Multiple Sequence Alignment X2s 2D prediction with energy and covariance ConStruct2.0 Thermodynamic controlled prediction of conserved secondary structure. Stochastic context free grammar(SCFG) STOCCFG webserver prediction of secondary structure of bacterial SSU rRNA Visualizing RnaViz loopDloop XRNA SStructView VizQFolder Rnadraw Others STRUCTURELAB Computational Approaches to RNA Structure Analysis NCRNASCAN structural RNA genefinder ESSA paRNAss Prediction of alternative RNA 2-D structure efn server Free energy and enthalpy tables for RNA folding -------------------------------------------------------------------------------- Motifs Searching in Sequences tRNAscan-SE Search Server Search for tRNA genes in genomic sequence RNAMOT A motif-bases comparaison of genomes STRUCT A Constraint Based Structure Description Language for Biosequences Rnabob tRNAscan-SE pol3scan FAStRNA COVE -------------------------------------------------------------------------------- Modeling, Analyzing and Visualizing Three-Dimensional Structure Visualizing VIsualize INSIGHT II MOLMOL RIBBON RASMOL VMD XMOL MOLSCRIPT RASTER3D MOLVIEW Cn3D GRASP GRASS SPOCK Modeling Mc-Sym 3.1 YAMMP NAB Pro Chemist Analysis MC-Annotate 3D RNA Structure analysis AMIGOS CURVE Naccess2.1.1 Solvent accessible area calculations Molecular Mechanics and Dynamics AMBER NAMD CHARMM -------------------------------------------------------------------------------- Last modified: September, 28 2000 by Guylaine Poisson [/url] [search]RNA informatics[/search] http://www-lbit.iro.umontreal.ca/RNA_Links/RNA.shtml [ Last edited by caucdenis on 2007-5-2 at 10:53 ] |
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