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on page 1 showing 10 out of 10 results

Cite this (CAZy- Carbohydrate Active Enzyme, RRID:SCR_012909)

URL: http://www.cazy.org

Resource Type: Resource, data or information resource, database

Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site.

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Cite this (Cell-PLoc, RRID:SCR_011966)

URL: http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc/

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

A package of web-servers for predicting subcellular localization of proteins in different organisms.

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Cite this (Eukaryotic Linear Motif, RRID:SCR_003085)

URL: http://elm.eu.org

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

Computational biology resource for investigating candidate functional sites in eukarytic proteins. Functional sites which fit to the description linear motif are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives. The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive.

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    IntAct

Cite this (IntAct, RRID:SCR_006944)

URL: http://www.ebi.ac.uk/intact

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

Open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. Direct user submissions of molecular interaction data are encouraged, which may be deposited prior to publication in a peer-reviewed journal. The IntAct Database contains (Jun. 2014): * 447368 Interactions * 33021 experiments * 12698 publications * 82745 Interactors IntAct provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows "zooming in" on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available.

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    mGOASVM

Cite this (mGOASVM, RRID:SCR_013098)

URL: http://bioinfo.eie.polyu.edu.hk/mGoaSvmServer/mGOASVM.html

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

Data analysis service for the prediction of multi-label protein subcellular localization based on gene ontology and support vector machines. Web services are also available.

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Cite this (NCBI Assembly Archive Viewer, RRID:SCR_012917)

URL: http://www.ncbi.nlm.nih.gov/Traces/assembly/assmbrowser.cgi

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

Graphical interface to contig and trace data in NCBI's Assembly Archive. The Archive links the raw sequence information found in the Trace Archive with assembly information found in publicly available sequence repositories (GenBank/EMBL/DDBJ). The Assembly Viewer allows a user to see the multiple sequence alignments as well as the actual sequence chromatogram.

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Cite this (NCBI Genome, RRID:SCR_002474)

URL: http://www.ncbi.nlm.nih.gov/genome

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

Database that organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations in six major organism groups: Archaea, Bacteria, Eukaryotes, Viruses, Viroids, and Plasmids. Genomes of over 1,200 organisms can be found in this database, representing both completely sequenced organisms and those for which sequencing is in progress. Users can browse by organism, and view genome maps and protein clusters. Links to other prokaryotic and archaeal genome projects, as well as BLAST tools and access to the rest of the NCBI online resources are available.

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Cite this (NCBI Taxonomy, RRID:SCR_003256)

URL: http://www.ncbi.nlm.nih.gov/taxonomy/

Resource Type: Resource, data or information resource, database

Database for a curated classification and nomenclature that contains the names of all organisms that are represented in the public sequence databases with at least one nucleotide or protein sequence. Data provided encompasses archaea, bacteria, eukaryota, viroids and viruses. The NCBI taxonomy database is not a primary source for taxonomic or phylogenetic information. Furthermore, the database does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts. Consequently, the NCBI taxonomy database is not a phylogenetic or taxonomic authority and should not be cited as such.

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    RefSeq

Cite this (RefSeq, RRID:SCR_003496)

URL: http://www.ncbi.nlm.nih.gov/RefSeq/

Resource Type: Resource, data or information resource, database

Collection of comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. It provides stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analysis. Included are sequences from plasmids, organelles, viruses, archaea, bacteria, and eukaryotes. Each RefSeq is constructed wholly from sequence data submitted to the International Nucleotide Sequence Database Collaboration (INSDC). Provides large, multi-species, curated sequence database representing separate but explicitly linked records from genomes to transcripts and translation products, as appropriate. Provides, for each included species, complete set of non-redundant, extensively cross-linked, and richly annotated nucleic acid and protein records.

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    SPInDel

Cite this (SPInDel, RRID:SCR_004509)

URL: http://www.portugene.com/SPInDel/SPInDel_webworkbench.html

Resource Type: Resource, software resource, data set, data or information resource

A multifunctional workbench for species identification using insertion/deletion variants. The SPInDel workbench provides a step-by-step environment for the alignment of target sequences, selection of informative hypervariable regions, design of PCR primers and the statistical validation of the species-identification process. It includes a large dataset comprising nearly 1,800 numeric profiles for the identification of eukaryotic, prokaryotic and viral species.

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