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It is a tool developed for RNR research that gives you the opportunity to retrieve RNR protein sequences from any organism that have been either experimentally characterised or predicted from genome sequence data. The RNR database contains a compilation of all published 3D structures of different RNR proteins as well as a compilation of all mutant proteins constructed including links to the relevant publication(s). RNRs by organism gives an overview of the entire database. Users can also search the database for occurrence of ribonucleotide reductases in taxonomic groups. The BLAST server of the RNR database allows sequences to be BLASTed against our database that contains RNR sequence, genomic, and species data.

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• SciCrunch
• 17 years ago - by Anonymous

Welcome to the computational genomics laboratory''s home page. Main research interests: computational biology, bioinformatics and systems biology applied to the study of the mechanisms underlying gene expression regulation. They also develop bioinformatic software aiming at helping the research community solve some problems.

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• SciCrunch
• 17 years ago - by Anonymous

It provides access to results from RNAi interference studies in C. elegans, including images, movies, phenotypes, and graphical maps. RNAiDB contains all published RNAi experiments in C. elegans that have been deposited in WormBase, including data from the literature and published large-scale RNAi studies. RNAi to gene mappings for all experiments have been re-analyzed using ePCR and/or a sliding n-mer window method to identify all genes in different genomic locations that may potentially be inhibited by each experiment. Gene maps showing canonical and putative alternate mappings are displayed graphically on RNAi Experiment and Gene/ORF card pages.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. It is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments (in species where more than one isolate has been fully sequenced) and contains translated genome sequences for all species. It has been created for two main purposes: to facilitate the comparative analysis of RNA viruses and to become a hub for other, more specialised virus Web sites.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 25, 2013. RISSC is a database of ribosomal 16S-23S spacer sequences intended mainly for molecular biology studies in typing, phylogeny and population genetics. Ribosomal spacers have proven to be extremely useful tools for typing and identifying closely related prokaryotes due to their high variability in size and/or sequence, much more so than the flanking 16S and 23S rRNA genes. These genes are commonly used to establish molecular relationships among microbes at a taxonomic level of species or higher (e.g genus, domain...). However their internal transcribed spacers (ITS) are much more useful to discriminate at the species or even strain level. Currently, many published papers are showing the growing importance of these regions of the ribosomal operon in these types of studies. A second, much shorter, ribosomal spacer can be found between rRNA genes 23S and 5S, also of phylogenetic interest. We intend to incorporate them into the database in the near future. By creating RISSC, our intention is to provide the scientific community with a comprehensive set of ribosomal spacer sequences, fully edited and characterized with a key feature as is the presence/absence of tRNA genes within them, ready to be used and compared with their own ITS sequences.

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• SciCrunch
• 17 years ago - by Anonymous

A partly-commercial resource that also supplies freeware to the general public. The freeware it supplies include a DNA trace viewer and editor (TraceEdit), MRSA strain/spa-typing software (SpaServer), and epidemiological typing software (EpiCompare). The SpaServer can be used to collate and harmonize data from various geographic regions. This WWW site is freely accessible to internet users and the spa-repeat sequences and the -types can be downloaded. Chromatograms of new spa-repeats and/or -types can be submitted online for inclusion into the reference database. Ridom TraceEdit is a cross-platform graphical DNA trace viewer and editor. TraceEdit displays the chromatogram files from Applied Biosystems automated sequencers and files in the Staden SCF format. Incorrect base calls can be edited and saved. The program Ridom EpiCompare can calculate various criteria for data of different typing techniques. It combines easy calculation with ease of data handling. Ridom EpiCompare can calculate the following parameters: *Typability is the percentage of distinct microbial strains which can be assigned a positive typing marker. *Reproducibility is the percentage of strains that give the same result on repeated testing. *Discriminatory power of a typing method is its ability to distinguish between unrelated strains. the an important ability of typing systems. *Typing system concordance helps to compare different independent typing systems.

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• SciCrunch
• 17 years ago - by Anonymous

A rice genome automated annotation system. This system integrates programs for prediction and analysis of protein-coding gene structure. Integrated softwares are coding region prediction programs ( GENSCAN, RiceHMM, FGENESH, MZEF ), splice site prediction programs (SplicePredictor ), homology search analysis programs ( Blast, HMMER, ProfileScan, MOTIF ), tRNA gene prediction program ( tRNAscan-SE ), repetitive DNA analysis programs ( RepeatMasker, Printrepeats ), signal scan search program ( Signal Scan ), protein localization site prediction program ( PSORT ), and program of classification and secondary structure prediction of membrane proteins ( SOSUI ). Blast against full-length cDNA sequences of japonica rice is integrated. The full-length rice cDNA sequence is provided by KOME database. Interpretation of the coding region is fully automated and gene prediction is accomplished without manual evaluation and modification. Therefore some differences exist between the predicted genes by the system and the manually predicted genes included in the GenBank entries. Please see "comparison table of gene prediction", http://RiceGAAS.dna.affrc.go.jp/rga-bin/col_accur.pl in detail. Further, a unique function is automatically assigned for predicted gene by GFSelector based on the protein homology of the gene. Additionally, the keyword search from the functions predicted by GFSelector is provided.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application for calculation of the restricted likelihood-ratio affected sib-pair test for linkage allowing for imprinting (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Memorial Sloan-Kettering Cancer Center''s ontology of surgical secondary events (adverse events).

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• SciCrunch
• 13 years ago - by Anonymous

A public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome. It is a compendium of rice genomic resources consisting of genetic markers, genome annotation, expressed sequence tags (ESTs), protein domains, gene ontology, plant stress-responsive genes, metabolic pathways and prediction of protein-protein interactions. RiceGeneThresher system integrates these diverse data sources and provides powerful web-based applications, and flexible tools for delivering customized set of biological data on rice. Its system supports whole-genome gene mining for QTL by using DNA marker intervals or genomic loci. RiceGeneThresher provides biologically supported evidences that are essential for targeting groups or networks of genes involved in controlling traits underlying QTL. Users can use it to discover and to assign the most promising candidate genes in preparation for the further gene function validation analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

A contig-oriented database for high-quality manual annotation of RGP, which can present non-redundant contig analyses by merging the accumulated PAC/BAC clones. As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results (30000 predicted genes.) The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome. Note that the annotation data of chromosomes 1, 3, 4 and 10 are restored from flat files of the public database. These basically contain the predicted genes information but not contain their evidence information.

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• SciCrunch
• 17 years ago - by Anonymous

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: Non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion. Rfam is also available via FTP. You can find data in Rfam in various ways... * Analyze your RNA sequence for Rfam matches * View Rfam family annotation and alignments * View Rfam clan details * Query Rfam by keywords * Fetch families or sequences by NCBI taxonomy * Enter any type of accession or ID to jump to the page for a Rfam family, sequence or genome

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• SciCrunch
• 17 years ago - by Anonymous

This database provides some information and resources related to LTR-retrotransposons in rice genome. The availability of the pseudomolecules of the Asian cultivated rice (Oryza sativa ssp. japonica cv. Nipponbare) allowed the construction, for the first time, of a non-redundant database of LTR retrotransposon sequences for an agronomically important plant species. 242 distinct families are curated, of which 194 have not been described elsewhere. These newly identified sequences, representing mainly low copy number elements, were identified by in-silico approaches. Reference molecules of each LTR retrotransposon family were characterized, annotated and deposited in RetrOryza. Further analysis will be focused on the identification and the annotation of LTR retrotransposons of several species within the Oryza genus.

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• SciCrunch
• 17 years ago - by Anonymous

It contains entries for refolding protocols for a wide range of proteins. REFOLD provides a means of dissminating refolding protocols and techniques to the scientific community. A large number of recombinant proteins expressed in bacteria are insoluble and thus require renaturation. Identifying optimal conditions and methodology for refolding can be time consuming and often rate-limiting. To this end, REFOLD was designed to assist in the design and implementation of methodologies for the in vitro refolding of proteins. The database contains heavily annotated entries for the refolding of a wide range of proteins which can be searched via multiple parameters using either simple or advanced search functions. The database can also be browsed by categories such as structural class, family, or refolding method. The web interface allows a detailed, sortable, spreadsheet-like list of results allowing quick visualisation of search results. Each entry contains detailed information regarding the protein of interest, methods and conditions employed, as well as reference and links to the relevant journal publication. Effective use of hyperlinks in results pages also allows useful browsing of entries for other proteins sharing similar properties or methods. REFOLD also provides analysis of the database through graphical representation of the data. The available graphs show the breakdown of refolding records in the database according to different parameters, such as refolding method, protein constructs and various refolding conditions. REFOLD graphs can be found here., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

• Organization
• SciCrunch
• 15 years ago - submitted by Andrea Stagg

A compilation of programmed; translational recoding events taken from the scientific literature and personal communications. The database deals with programmed ribosomal frameshifting, codon redefinition and translational bypass occurring in a variety of organisms. The entries for each event include the sequences of the corresponding genes, their encoded proteins for both the normal and alternate decoding, the types of the recoding events involved, trans-factors and cis-elements that influence recoding.

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• SciCrunch
• 17 years ago - by Anonymous

Database of information about restriction enzymes and related proteins containing published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Several tools are available including REBsites, BLAST against REBASE, NEBcutter and REBpredictor. Putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. REBASE is updated daily and is constantly expanding. Users may submit new enzyme and/or sequence information, recommend references, or send them corrections to existing data. The contents of REBASE may be browsed from the web and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email.,

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented April 14, 2017. The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers, QTL's, etc. that is localized to chromosome. The database is dedicated to rat gene nomenclature and should be consulted for queries in such matters.

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• SciCrunch
• 17 years ago - by Anonymous

This database houses information on biological resources ranging from transcriptome to phenome, including RIKEN Arabidopsis full-length (RAFL) complementary DNAs (cDNAs), their promoter regions, Dissociation (Ds) transposon-tagged lines and expression data from microarray experiments. RARGE provides tools for searching by resource code, sequence homology or keyword, and rapid access to detailed information on the resources. We have isolated 245 946 RAFL cDNA clones and collected 11 933 transposon-tagged lines, which are available from the RIKEN Bioresource Center and are stored in RARGE.

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• SciCrunch
• 17 years ago - by Anonymous

A new source of RESP or ESP atomic charge values for small structures or model systems. Its goals are multiple. R.E.DD.B. freely stores and distributes derived RESP or ESP charges of high quality and high reproduciblility within force field library(ies) in the scientific community. However, R.E.DD.B. can also be seen as a tool devoted to reproduce, compare, criticize and improve the different RESP and ESP models. As indicated by its name, R.E.DD.B. deals _only_ with RESP or ESP charges, and not with other types of atomic charges (Mulliken, Gasteiger or Bader analysis...). As previously said, many different procedures are used to derive such RESP or ESP charges, and the charge values are affected by many parameters (Quantum Mechanics programs, algorithms, molecular orientation, molecular conformation, human errors, etc..). Thus, R.E.DD.B. not only stores RESP or ESP charge values, but also the structures and information about the procedure used to derive the reported charge values. Two types of "projects" can be found in R.E.DD.B. - A WHOLE MOLECULE "project", which corresponds to an intact (un-broken) molecule. Examples are small organic or inorganic molecules such as solvent (DMSO, ethanol, cyclohexane etc...), and ligands of proteins or nucleic acids. - A MOLECULE FRAGMENT "project", which corresponds to a part (or fragment) of an organic or inorganic macro-molecule. This means that some atoms have to be removed from the structure(s) used in the charge derivation process to lead to the target fragment(s). Examples are amino-acid (AA) fragments 'NH-CH(R)-CO' where the atomic charges are generally derived using capped amino acids 'ACE-AA-NME', nucleotide fragments originating from the fusion between dimethylphosphate and the corresponding nucleosides, or monosaccharide fragments. These fragments are generally compatible with previously existing ones (available in force field topology databases), and used to construct macro-molecules such as proteins, nucleic acids or polysaccharides.

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• SciCrunch
• 17 years ago - by Anonymous