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on page 1 showing 20 out of 91 results

Cite this (AmphoraNet, RRID:SCR_005009)

URL: http://amphoranet.pitgroup.org/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data. It is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample.

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Cite this (Aspergillus Genomes, RRID:SCR_001880)

URL: http://www.aspergillus-genomes.org.uk/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

A resource for viewing annotated genes arising from various Aspergillus sequencing and annotation projects, resulting from the merging of Central Aspergillus Data REpository (CADRE) and The Aspergillus Website, which took place in June 2008. The principal role of CADRE is to aid the Aspergillus research community by managing Aspergillus genome data and by providing visualization tools, ranging from relatively simple annotation displays to more complex data integration displays. In contrast, The Aspergillus Website provides a range of information to the medical community (i.e., clinicians, patients and scientists) regarding the genus Aspergillus and the diseases, such as Aspergillosis, that it can cause. CADRE has been implemented using the Ensembl v22 suite. This suite comprises: * a database schema, which has been devised for storing annotated eukaryotic genomes. The schema is implemented with the MySQL relational database management system. * several specialized programming modules for building interfaces (i.e., BioPerl and Ensembl API modules). * a series of programs (i.e., Perl CGI scripts using the API modules) for viewing genomic data within a web browser.

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    BeeBase

Cite this (BeeBase, RRID:SCR_008966)

URL: http://hymenopteragenome.org/beebase/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, data set, service resource, data or information resource

Gene sequences and genomes of Bombus terrestris, Bombus impatiens, Apis mellifera and three of its pathogens, that are discoverable and analyzed via genome browsers, blast search, and apollo annotation tool. The genomes of two additional species, Apis dorsata and A. florea are currently under analysis and will soon be incorporated.

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    BioRep

Cite this (BioRep, RRID:SCR_004907)

URL: http://www.biorep.it/en

Resource Type: Resource, material analysis service, analysis service resource, biomaterial supply resource, biospecimen repository, production service resource, tissue bank, material service resource, service resource, storage service resource, cell repository, biomaterial analysis service, material resource, biomaterial manufacture, material storage repository

Offer biorepository services to public and private research institutes, to the highest standards of quality and safety with the aim of contributing to the advancement of medical research and scientific discovery. The BioRep Cell Repository establishes, maintains and distributes cell line cultures as well as DNA derived from these cultures. The scientific and business affiliation between BioRep and Coriell allows access to more than a million types of cell vials, stored in liquid nitrogen. Cells that have been stored for nearly 50 years, are still viable and available for research purposes today. Thanks to an exclusive agreement with the Coriell Institute for Medical Research, the oldest and largest biorepository of the world, BioRep is specialized in cell lines preparation, in nucleic acid extraction and long term storage in liquid nitrose (-196 degrees C) and in refrigerators (-80 degrees C) of any kind of biosamples, using procedures and standards developed by the Coriell in over 50 years of activity. BioRep and Coriell together constitute one of the few Global Biorepository able to serve the pharmaceutical industries for world wide clinical trials. BioRep facility is specifically designed to give the utmost efficiency and security by implementing Coriell procedures and standards. The BioRep Tissue Repository provides safe and secure storage of tissue specimens as required for medical research and scientific investigation. All tissues are preserved with the most current preservation techniques and processes. In addition to the storage service, BioRep provides Cell Biology, Molecular Biology, Microbiology services developed in ISO 9001:2008 certified laboratories.

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Cite this (BiSearch: Primer Design and Search Tool, RRID:SCR_002980)

URL: http://bisearch.enzim.hu

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

BiSearch is a primer-design algorithm for DNA sequences. It may be used for both bisulfite converted as well as for original not modified sequences. You can search various genomes with the designed primers to avoid non-specific PCR products by our fast ePCR method. This is especially recommended when primers are designed to amplify the highly redundant bisulfite treated sequences. It has the unique property of analyzing the primer pairs for mispriming sites on the bisulfite-treated genome and determines potential non-specific amplification products with a new search algorithm. The options of primer-design and analysis for mispriming sites can be used sequentially or separately, both on bisulfite-treated and untreated sequences. In silico and in vitro tests of the software suggest that new PCR strategies may increase the efficiency of the amplification.

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    BLASTN

Cite this (BLASTN, RRID:SCR_001598)

URL: http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch

Resource Type: Resource, data analysis service, database, analysis service resource, production service resource, service resource, data or information resource

Web application to search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast.

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    BLASTX

Cite this (BLASTX, RRID:SCR_001653)

URL: http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&BLAST_PROGRAMS=blastx&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome

Resource Type: Resource, data analysis service, database, analysis service resource, production service resource, service resource, data or information resource

Web application to search protein databases using a translated nucleotide query. Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence and is used extensively in analyzing EST sequences. This search is more sensitive than nucleotide blast since the comparison is performed at the protein level.

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    BRENDA

Cite this (BRENDA, RRID:SCR_002997)

URL: http://www.brenda-enzymes.org/

Resource Type: Resource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, data repository, data or information resource

Main database of functional biochemical and molecular enzyme data that provides access to seven interconnected databases. It contains 2.7 million manually annotated data on enzyme occurrence, function, kinetics and molecular properties. The majority of the data are manually extracted from the primary literature. Each entry is connected to a reference and the source organism. Enzyme ligands are stored with their structures and can be accessed via their names, synonyms or via a structure search. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are based on text mining methods and represent a complete survey of PubMed abstracts with information on enzymes in different organisms, tissues or organelles. The supplemental database DRENDA provides more than 910 000 new EC number-disease relations in more than 510 000 references from automatic search and a classification of enzyme-disease-related information. KENDA (Kinetic ENzyme DAta), a new amendment extracts and displays kinetic values from PubMed abstracts. The integration of the EnzymeDetector offers an automatic comparison, evaluation and prediction of enzyme function annotations for prokaryotic genomes. The biochemical reaction database BKM-react contains non-redundant enzyme-catalyzed and spontaneous reactions and was developed to facilitate and accelerate the construction of biochemical models. The content covers information on function, structure, occurrence, preparation and application of enzymes as well as properties of mutants and engineered variants. BRENDA provides viewing options such as the display of the statistics of functional parameters and the 3D view of protein sequence and structure features. Furthermore a ligand summary shows comprehensive information on the BRENDA ligands. The enzymes are linked to their respective pathways and can be viewed in pathway maps. The disease text mining part is strongly enhanced. It is possible to submit new, not yet classified enzymes to BRENDA, which then are reviewed and classified by the International Union of Biochemistry and Molecular Biology. A new SBML output format of BRENDA kinetic data allows the construction of organism-specific metabolic models. The enzymes are classified according to the Enzyme Commission list of enzymes. Some 5000 different enzymes are covered. Frequently enzymes with very different properties are included under the same EC number. Although they intend to give a representative overview on the characteristics and variability of each enzyme the Handbook is not a compendium. The reader will have to go to the primary literature for more detailed information. Naturally it is not possible to cover all the numerous literature references for each enzyme (for some enzymes up to 40000) if the data representation is to be concise as is intended. The data collection is being developed into a metabolic network information system with links to Enzyme expression and regulation information. BRENDA SOAP Webservice is available.

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    CCTOP

Cite this (CCTOP, RRID:SCR_016963)

URL: http://cctop.enzim.ttk.mta.hu/

Resource Type: Resource, data access protocol, production service resource, web service, analysis service resource, service resource, software resource

Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative ? helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them.

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Cite this (COnsensus-DEgenerate Hybride Oligonucleotide Primers, RRID:SCR_002875)

URL: http://blocks.fhcrc.org/blocks/codehop.html

Resource Type: Resource, data analysis service, data analysis software, data processing software, production service resource, analysis service resource, software application, service resource, software resource

This COnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategy has been implemented as a computer program that is accessible over the World-Wide Web and is directly linked from the BlockMaker multiple sequence alignment site for hybrid primer prediction beginning with a set of related protein sequences. This is a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region and a longer 5' consensus clamp region. Only 3-4 highly conserved amino acid residues are necessary for design of the core, which is stabilized by the clamp during annealing to template molecules. During later rounds of amplification, the non-degenerate clamp permits stable annealing to product molecules. The researchers demonstrate the practical utility of this hybrid primer method by detection of diverse reverse transcriptase-like genes in a human genome, and by detection of C5 DNA methyltransferase homologs in various plant DNAs. In each case, amplified products were sufficiently pure to be cloned without gel fractionation. Sponsors: This work was supported in part by a grant from the M. J. Murdock Charitable Trust and by a grant from NIH. S. P. is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation.

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    CRISPR-P

Cite this (CRISPR-P, RRID:SCR_016941)

URL: http://crispr.hzau.edu.cn/CRISPR/

Resource Type: Resource, data access protocol, production service resource, analysis service resource, web service, service resource, software resource

Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment.

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    DAM-Bio

Cite this (DAM-Bio, RRID:SCR_006226)

URL: http://athina.biol.uoa.gr/DAM-Bio/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, service resource, portal, data or information resource

An integrated environment designed to support protein sequence and structure analysis on the web.

  • From Current Category

Cite this (Database of Interacting Proteins, RRID:SCR_003167)

URL: http://dip.doe-mbi.ucla.edu/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, storage service resource, data repository, data or information resource

Database to catalog experimentally determined interactions between proteins combining information from a variety of sources to create a single, consistent set of protein-protein interactions that can be downloaded in a variety of formats. The data were curated, both, manually and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks. Tools are available to analyze, visualize and integrate user's own experimental data with the information about protein-protein interactions available in the DIP database. The DIP database lists protein pairs that are known to interact with each other. By interact they mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organization and complexity of the protein interaction network at the cellular level. Registration is required to gain access to most of the DIP features. Registration is free to the members of the academic community. Trial accounts for the commercial users are also available.

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    DIALIGN

Cite this (DIALIGN, RRID:SCR_003041)

URL: http://bibiserv.techfak.uni-bielefeld.de/dialign/

Resource Type: Resource, data analysis service, data access protocol, production service resource, analysis service resource, web service, service resource, software resource

Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/

  • From Current Category

Cite this (DictyBase, RRID:SCR_006643)

URL: http://dictybase.org/

Resource Type: Resource, data analysis service, organism supplier, database, analysis service resource, biomaterial supply resource, biospecimen repository, production service resource, service resource, storage service resource, material storage repository, material resource, data or information resource

Model organism database for the social amoeba Dictyostelium discoideum that provides the biomedical research community with integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a ''''reference genome'''' in the Amoebozoa clade. They highlight several new features in the present update: (i) new annotations; (ii) improved interface with web 2.0 functionality; (iii) the initial steps towards a genome portal for the Amoebozoa; (iv) ortholog display; and (v) the complete integration of the Dicty Stock Center with dictyBase. The Dicty Stock Center currently holds over 1500 strains targeting over 930 different genes. There are over 100 different distinct amoebozoan species. In addition, the collection contains nearly 600 plasmids and other materials such as antibodies and cDNA libraries. The strain collection includes: * strain catalog * natural isolates * MNNG chemical mutants * tester strains for parasexual genetics * auxotroph strains * null mutants * GFP-labeled strains for cell biology * plasmid catalog The Dicty Stock Center can accept Dictyostelium strains, plasmids, and other materials relevant for research using Dictyostelium such as antibodies and cDNA or genomic libraries.

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Cite this (DictyOGlyc, RRID:SCR_001600)

URL: http://www.cbs.dtu.dk/services/DictyOGlyc/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

Server that produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.

  • From Current Category

Cite this (DIG IT - Database of Immunoglobulins and Integrated Tools, RRID:SCR_005924)

URL: http://www.biocomputing.it/digit/index.php

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

The Database of Immunoglobulins and Integrated Tools (DIG IT) is an integrated resource storing sequences of annotated immunoglobulin variable domains of NCBI database and enriched with tools for searching and analyzing them. It contains 145759 heavy chain sequences and 71404 light chain sequences (47168 kappa type and 24236 lambda type) with assigned canonical structures for the hypervariable loops and the data on the type of antigen as well as the pairing information of immunoglobulin heavy and light chains (9672 total pairs). The user can input the immunoglobulin variable domain sequence (amino acid or nucleotide) of interest (heavy chain variable domain sequence; light chain variable domain sequence or both) to retrieve the closest sequences (sorted according to e-value) with complete annotation. The user can also directly query the database by antigen type, canonical structure, germline family in accordance to the requirements.

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    DREME

Cite this (DREME, RRID:SCR_016860)

URL: http://meme-suite.org/tools/dreme

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

Software tool to discover short, ungapped motifs (recurring, fixed-length patterns) that are relatively enriched in sequences compared with shuffled sequences or control sequences (sample output from sequences).

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Cite this (DTU Center for Biological Sequence Analysis, RRID:SCR_003590)

URL: http://www.cbs.dtu.dk/index.shtml

Resource Type: Resource, topical portal, data access protocol, production service resource, analysis service resource, training resource, data analysis service, data set, web service, service resource, portal, software resource, data or information resource

The Center for Biological Sequence Analysis of the Technical University of Denmark conducts basic research in the field of bioinformatics and systems biology and directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. A large number of computational methods have been produced, which are offered to others via WWW servers. Several data sets are also available. The center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. The on-line prediction services at CBS are available as interactive input forms. Most of the servers are also available as stand-alone software packages with the same functionality. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services. The center also educates engineering students in biotechnology and systems biology and offers a wide range of courses in bioinformatics, systems biology, human health, microbiology and nutrigenomics.

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    Ensembl

Cite this (Ensembl, RRID:SCR_002344)

URL: http://www.ensembl.org/

Resource Type: Resource, data analysis service, data access protocol, database, web service, production service resource, analysis service resource, catalog, service resource, software resource, data or information resource

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

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