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on page 1 showing 20 out of 367 results

Cite this (ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters, RRID:SCR_002276)

URL: http://genome.imim.es/datasets/abs2005/index.html

Resource Type: Resource, data or information resource, database

Public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken. For each regulatory site, the position, the motif and the sequence in which the site is present are available in a simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments and graphical dotplots are also available.

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    ADGO

Cite this (ADGO, RRID:SCR_006343)

URL: http://www.btool.org/ADGO2

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

A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets.

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    Aegean

Cite this (Aegean, RRID:SCR_015965)

URL: http://standage.github.io/AEGeAn

Resource Type: Resource, data analysis software, data processing software, software application, sequence analysis software, software resource, software toolkit

Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more.

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Cite this (AffyExpress, RRID:SCR_001321)

URL: http://www.bioconductor.org/packages/release/bioc/html/AffyExpress.html

Resource Type: Resource, software resource

Software package for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.

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Cite this (AIDA Toolkit, RRID:SCR_005914)

URL: https://adaptivedisclosure.wordpress.com/aida/

Resource Type: Resource, software resource, software toolkit, data access protocol, web service

A generic set of components that can perform a variety of tasks, such as learn new pattern recognition models, perform specialized search on resource collections, and store knowledge in a repository. W3C standards are used to make data accessible and manageable with semantic web technologies such as OWL, RDF(S), and SKOS. The AIDA Toolkit is directed at groups of knowledge workers that cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. The server offers services for: text indexing and statistics, metadata storage and querying, thesaurus reasoning, annotation, text retrieval, spelling correction, synonym detection, and model learning.

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Cite this (Algal Functional Annotation Tool, RRID:SCR_012034)

URL: http://pathways.mcdb.ucla.edu/algal/

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

Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest.

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Cite this (Alizadehlab: MeeboChip and HeeboChip Open Source Project, RRID:SCR_008384)

URL: http://alizadehlab.stanford.edu/

Resource Type: Resource, data or information resource, database

This is an open-source Mouse Exonic Evidence-Based Oligonucleotide Chip (MEEBOChip), and are in the process of building the human counterpart, HEEBOChip. The set of 70mers for MEEBOChip is already available from Illumina, Inc., with synthesis of HEEBOChip 70mers in progress. Both arrays are based on a novel selection of exonic long-oligonucleotides (70-mers) from a genomic annotation of the corresponding complete genome sequences, using a transcriptome-based annotation of exon structure for each genomic locus. Using a combination of existing and custom-tailored tools and datasets (including millions of mRNA and EST sequences), we built and performed a systematic examination of transcript-supported exon structure for each genomic locus at the base-pair level (i.e., exonic evidence). This strategy allowed them to select both constitutive and in many cases alternative exons for nearly every gene in the corresponding genome (e.g., protocadherin locus), allowing an unprecedented exploration of human and mouse biology. Furthermore, they used experimentally derived data to hone the selection of these 70mers, helping maximize their performance under typical fluorescent labeling and hybridization conditions. Specifically, they applied and refined the ArrayOligoSelector algorithm from Joe DeRisis laboratory to select 70mers, considering not only their uniqueness (i.e., hybridization specificity) within the content of the entire genome, but also to overcome the known biases of labeling and hybridization methods (e.g., 3-biased reverse transcription and in vitro transcription reactions).

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Cite this (Allen Brain Atlas API, RRID:SCR_005984)

URL: http://www.brain-map.org/api/index.html

Resource Type: Resource, software resource, software application, source code

API and demo application for accessing the Allen Brain Atlas Mouse Brain data. Data available via the API includes download high resolution images, expression data from a 3D volume, 3D coordinates of the Allen Reference Atlas, and searching genes with similar gene expression profiles using NeuroBlast. Data made available includes: * High resolution images for gene expression, connectivity, and histology experiments, as well as annotated atlas images * 3-D expression summaries registered to a reference space for the Mouse Brain and Developing Mouse Brain * Primary microarray results for the Human Brain and Non-Human Primate * RNA sequencing results for the Developing Human Brain * MRI and DTI files for Human Brain The API consists of the following resources: * RESTful model access * Image download service * 3-D expression summary download service * Differential expression search services * NeuroBlast correlative searches * Image-to-image synchronization service * Structure graph download service

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Cite this (Alt Event Finder, RRID:SCR_001846)

URL: http://compbio.iupui.edu/group/6/pages/alteventfinder

Resource Type: Resource, software resource

Software tool for deriving data-driven alternative splicing (AS) events from RNA-seq data. It analyses the transcripts built by Cufflinks or Scripture and outputs AS event annotations which is compatible with MISO. It can be used for annotating novel AS events from a well-annotated species such as human. It can also be used for species of which known AS event annotation is not available. The current release (v0.1) supports skipped exon events only.

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Cite this (AltSplice Database of Alternative Spliced Events, RRID:SCR_008162)

URL: http://www.ebi.ac.uk/asd/altsplice/index.html

Resource Type: Resource, data or information resource, database

AltSplice is a computer generated high quality data set of human transcript-confirmed splice patterns, alternative splice events, and the associated annotations. This data is being integrated with other data that is generated by other members of the ASD consortium. The ASD project will provide the following in its three year duration: -human curated database of alternative spliced genes and their properties -a computer generated database of alternatively spliced genes and their properties -the integration of the above and newly found knowledge in a user-friendly interface and research workbench for both bioinformaticists and biologists -DNA chips that are based on the data in the above databases -the DNA chips will be used to test against predisposition for and diagnoses of human diseases ASD aims to analyse this mechanism on a genome-wide scale by creating a database that contains all alternatively spliced exons from human, and other model species. Disease causing mutations seem to induce aberrations in the process of splicing and its regulation. The ASD consortium will develop a DNA microarray (chip) that contains cDNAs of all the splicing regulatory proteins and their isoforms, as well as a chip that contains a number of disease relevant genes. We will concentrate on three models of disease (breast cancer, FTDP-17, male infertility) in which a connection between mis-splicing and a pathological state has been observed. Finally, these chips will be developed as demonstrative kits to detect predisposition for and diagnosis of such diseases. Categories: Nucleotide Sequences: Gene Structure, Introns and Exons, & Splice Sites Databases

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Cite this (AlzSWAN Knowledge Base, RRID:SCR_003017)

URL: http://hypothesis.alzforum.org/

Resource Type: Resource, portal, knowledge environment, community building portal, knowledgebase, data or information resource

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A community-driven knowledgebase of Alzheimer disease, in which researchers can annotate scientific claims, data, and information, putting these into the context of testable hypotheses and treatment discovery. This SWAN project adds a collection of hand-curated hypotheses to a research paper, which are then related through a set of discourse relationships. They can be browsed and relations between claims, as well as support networks for a specific claim, are made and visualized. AlzSWAN is where you explore scientific knowledge about Alzheimer disease and share your own ideas, comments and questions in a semantically structured system. AlzSWAN is enabled by Semantic Web technology, a new standard for knowledge organization and transfer on the Web. AlzSWAN organizes and manages knowledge using formal knowledge descriptions called ontologies. Using these formal knowledge descriptions, they can tie statements made in scientific publications or on the Web to scientific evidence, biological terminologies, and knowledgebases, and to claims and counterclaims made by other researchers.

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    AmiGO

Cite this (AmiGO, RRID:SCR_002143)

URL: http://amigo.geneontology.org/

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

Official Web-based tools for searching and browsing the Gene Ontology database, which consists of a controlled vocabulary of terms covering biological concepts, and a large number of genes or gene products whose attributes have been annotated using GO terms. It can be accessed online at the main installation or deployed locally. The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. AmiGO can be used to:
* search for a gene or gene product, or a list of gene or gene products, and view the GO term associations
* perform a sequence identity BLAST search and view the GO term associations for the genes or proteins returned
* search for GO terms and view the genes or gene products they are annotated to
* browse the GO ontology and view terms
* the slimmer tool can be used to map the granular annotations of the query set of genes to one or more high-level
* term enrichment tool is used to discover what a set of genes may have in common by examining annotations and finding significant shared GO terms.
* GOOSE is for advanced users who want to run custom SQL queries against the GO database.

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Cite this (Ancient conserved untranslated sequences, RRID:SCR_008130)

URL: http://pbil.univ-lyon1.fr/acuts/ACUTS.html

Resource Type: Resource, data or information resource, database

THIS RESOURCE IS NO LONGER IN SERVICE, Documented on August 12, 2014. Database that identifies new regulatory elements in untranslated regions of protein-coding genes (5 prime flanks, 5 prime UTRs, introns, 3 prime UTRs and 3 prime flanks). The analyses is focused on genes from metazoan species (essentially vertebrates, insects and nematodes). Information on highly conserved regions (sequences, alignments, annotations, bibliographic references) are compiled. Currently 176 out of 326 detected highly conserved regions (HCRs) have been analyzed and incorporated in the database. You can also access the list of annotated conserved elements and the list of conserved elements that remain to be processed. Their approach is based on comparative sequence analysis, for the identification of phylogenetic footprints.

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Cite this (ANNOgesic, RRID:SCR_016326)

URL: https://github.com/Sung-Huan/ANNOgesic

Resource Type: Resource, standalone software, data processing software, software application, data analysis software, software resource, software toolkit

Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.

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    Annotare

Cite this (Annotare, RRID:SCR_000319)

URL: http://code.google.com/p/annotare/

Resource Type: Resource, software resource, software application, standalone software

A software tool for annotating biomedical investigations and the resulting data, then producing a MAGE-TAB file. This software is a standalone desktop which features: an editor function, an annotation modifier, incorporation of terms from biomedical ontologies, standard templates for common experiment types, a design aid to help create a new document, and a validator that checks for syntactic and semantic violations.

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Cite this (A.nnotate, RRID:SCR_002839)

URL: http://a.nnotate.com/

Resource Type: Resource, software resource, service resource, commercial organization, storage service resource

An online annotation, collaboration and indexing system for documents and images, supporting PDF and MS Office formats. Instead of emailing different versions of a document back and forth you can all comment on a single read-only copy online. Unlike online word processors, the document is displayed in high quality with fonts and layout just like the printed version. It is easy to use and runs in all common web browsers, with no software or plugins to install. Hosted solutions are available for individuals and workgroups. For enterprise users the full system is available for local installation. Special discounts apply for educational use. The FREE hosted solution offers single-user accounts for uploading up to 30 pages per month. Documents can be shared with any number of annotators.

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Cite this (Annotation Ontology, RRID:SCR_002862)

URL: http://code.google.com/p/annotation-ontology/

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

A vocabulary for performing several types of annotation - comment, entities annotation (or semantic tags), textual annotation (classic tags), notes, examples, erratum... - on any kind of electronic document (text, images, audio, tables...) and document parts. AO is not providing any domain ontology but it is fostering the reuse of the existing ones for not breaking the principle of scalability of the Semantic Web.

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Cite this (Annotator, RRID:SCR_000611)

URL: http://okfnlabs.org/annotator/

Resource Type: Resource, software resource

The Annotator is an open-source JavaScript library and tool that can be added to any webpage to make it annotatable. Annotations can have comments, tags, users and more. Moreover, the Annotator is designed for easy extensibility so its a cinch to add a new feature or behavior. Adding annotation to your webpage using the Annotator is easy. Full instructions are in the Getting Started section of the docs, but it is just two short steps. First, you need to download the Annotator library (or link to the hosted version), include it on your page along with jQuery. Then add the following line to initialize the annotator. $("#content").annotator(); Plug-ins can be included for adding functionality such as user accounts, tags, filtering and formatting. You'll need to store your data somewhere, luckily we've made this very simple to do using AnnotateIt, a hosted web service for storing annotations. Alternatively if you'd like to integrate the annotator with your own storage system check out the Docs for more information on the annotation format and store plugin. The bookmarklet is a simple tool that allows you to add the annotator to any webpage and save your annotations to AnnotateIt. Check it out at http://annotateit.org/.

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Cite this (Annozilla (Annotea on Mozilla), RRID:SCR_007549)

URL: http://annozilla.mozdev.org/

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

The Annozilla project was designed to view and create annotations associated with a web page, as defined by the W3C Annotea project. Annotations are stored as RDF on a server, using XPointer (or at least XPointer-like constructs) to identify the region of the document being annotated. Additionally, the Annozilla source code is available. The intention of Annozilla is to use Mozilla''''s native facilities to manipulate annotation data - its built-in RDF handling to parse the annotations, and nsIXmlHttpRequest to submit data when creating annotations. To use Annozilla, you will need to install the packages, get set up with a user account with an annotation server (e.g., the W3C test server), and then you should be ready to start using the extension.

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    AnnTools

Cite this (AnnTools, RRID:SCR_005170)

URL: http://anntools.sourceforge.net/

Resource Type: Resource, software resource

Software tool for annotating single nucleotide substitutions (SNP/SNV), small insertions/deletions (indels), and copy number variations (CNV) calls generated from sequencing and microarray data. Only human genome build 37/hg19 can be annotated at this time.

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