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on page 1 showing 20 out of 153 results from 1 sources

Cite this (1000 Genomes: A Deep Catalog of Human Genetic Variation, RRID:SCR_006828)

URL: http://www.1000genomes.org/

Resource Type: Resource, organization portal, database, consortium, data set, portal, data or information resource

International collaboration producing an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts, in an effort to provide a foundation for investigating the relationship between genotype and phenotype. The genomes of about 2500 unidentified people from about 25 populations around the world were sequenced using next-generation sequencing technologies. Redundant sequencing on various platforms and by different groups of scientists of the same samples can be compared. The results of the study are freely and publicly accessible to researchers worldwide. The consortium identified the following populations whose DNA will be sequenced: Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Gujarati Indians in Houston; Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles; and people of African ancestry in the southwestern United States. The goal Project is to find most genetic variants that have frequencies of at least 1% in the populations studied. Sequencing is still too expensive to deeply sequence the many samples being studied for this project. However, any particular region of the genome generally contains a limited number of haplotypes. Data can be combined across many samples to allow efficient detection of most of the variants in a region. The Project currently plans to sequence each sample to about 4X coverage; at this depth sequencing cannot provide the complete genotype of each sample, but should allow the detection of most variants with frequencies as low as 1%. Combining the data from 2500 samples should allow highly accurate estimation (imputation) of the variants and genotypes for each sample that were not seen directly by the light sequencing. All samples from the 1000 genomes are available as lymphoblastoid cell lines (LCLs) and LCL derived DNA from the Coriell Cell Repository as part of the NHGRI Catalog. The sequence and alignment data generated by the 1000genomes project is made available as quickly as possible via their mirrored ftp sites. ftp://ftp.1000genomes.ebi.ac.uk ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes

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Cite this (Adult Mouse Anatomy Ontology, RRID:SCR_006568)

URL: http://www.informatics.jax.org/searches/AMA_form.shtml

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

Ontology that organizes anatomical structures for the adult mouse (Theiler stage 28) spatially and functionally, using ''is a'' and ''part of'' relationships. The ontology is used to describe expression data for the adult mouse and phenotype data pertinent to anatomy in standardized ways. The browser can be used to view anatomical terms and their relationships in a hierarchical display.

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Cite this (Alliance of Genome Resources , RRID:SCR_015850)

URL: http://www.alliancegenome.org/

Resource Type: Organization, organization portal, consortium, service resource, portal, access service resource, data or information resource

Organization that aims to develop and maintain sustainable genome information resources to promote understanding of the genetic and genomic basis of human biology, health, and disease. The Alliance is composed of FlyBase, Mouse Genome Database (MGD), the Gene Ontology Consortium (GOC), Saccharomyces Genome Database (SGD), Rat Genome Database (RGD), WormBase, and the Zebrafish Information Network (ZFIN).

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    AMAP

Cite this (AMAP, RRID:SCR_015969)

URL: http://code.google.com/p/amap-align/

Resource Type: Resource, image analysis software, data processing software, source code, alignment software, software application, software resource

Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method.

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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 (Ancestrymap, RRID:SCR_004353)

URL: http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html

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

Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux.

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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 (Antibody Validation Database, RRID:SCR_011996)

URL: http://compbio.med.harvard.edu/antibodies/

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

The aim of this site is to collect and to share experimental results on antibodies that would otherwise remain in laboratories, thus aiding researchers in selection and validation of antibodies.

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Cite this (ArrayExpress, RRID:SCR_002964)

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

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

Database of functional genomics experiments including gene expression where you can query and download data collected to MIAME and MINSEQE standards. It includes gene expression data from microarray and high throughput sequencing studies. Gene Expression Atlas contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. The ArrayExpress Archive is one of the three international public repositories of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus. The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy. The Repository contains data from over 47787 experiments comprising approximately 1361377 assays (March 2014). The majority of the data are array based, but other data types are included, including ultra high-throughput sequencing transcriptomics and epigenetic data. All the data and array designs in ArrayExpress are available for direct download in a number of different formats. Submissions are welcome.

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Cite this (ASprofile, RRID:SCR_001833)

URL: http://ccb.jhu.edu/software/ASprofile/

Resource Type: Resource, software resource

A suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data.

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    Bamtools

Cite this (Bamtools, RRID:SCR_015987)

URL: https://github.com/pezmaster31/bamtools/wiki

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

Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies.

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Cite this (Baylor College of Medicine Human Genome Sequencing Center, RRID:SCR_013605)

URL: http://www.hgsc.bcm.tmc.edu/

Resource Type: Resource, topical portal, portal, data or information resource

Center for high-throughput DNA sequence generation and the accompanying analysis. The center operates multiple sequencing platforms (ABI Sanger and SOLid, 454 Life Sciences and Solexa/Illumina). The sequence data generated by these machines is analyzed in a complex bioinformatics pipeline, and the data are deposited regularly in the public databases at the National Center for Biotechnology Information (NCBI). The BCM-HGSC is also involved in developing the next generation of DNA sequencing and bioinformatics technologies that will allow greater scientific advances in the future. The center was established when the National Human Genome Research Institute (NHGRI) designated Baylor College of Medicine as one of six pilot programs for the final phases of the Human Genome Project (HGP). Later on, it was chosen as one of three sites from the pilot program to complete the HGP. The HGP is now in a new phase of exploring individual DNA sequence variation and its association with human diseases including Parkinsons disease, childhood diabetes, bipolar disorder, schizophrenia, heart disease, premature birth, epilepsy, autism as well as breast, prostate, brain, pancreatic and bladder cancer. In addition the HGSC is characterizing normal genetic variation in human populations. The results are anticipated to change the way scientists understand disease and other life processes. Since the completion of the human genome project, the HGSC has sequenced many other genomes, including the mouse, rat, fruit fly, rhesus monkey, honey bee, sea urchin, marmoset, orangutan, and cow. In addition, sequencing projects are currently under way for many other species, including the acorn worm, wallaby, hyrax, megabat, dolphin, pea aphid, red flour beetle, nasonia wasp, gibbon, baboon, and over two hundred different microbial organisms. The genomes of these other organisms will help us predict where genes are located in human chromosomes, and will lead to a better understanding of how genomes have evolved.

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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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    Belvu

Cite this (Belvu, RRID:SCR_015989)

URL: http://www.sanger.ac.uk/science/tools/seqtools

Resource Type: Resource, alignment software, image analysis software, data processing software, software resource, software application

Software for multiple sequence alignment viewing, editing and phylogeny. It includes a set of user-configurable modes to color residues used to create high-quality reference alignments.

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Cite this (Berkeley Bioinformatics Open-Source Projects, RRID:SCR_006704)

URL: http://www.berkeleybop.org/

Resource Type: Resource, software resource, topical portal, portal, data or information resource

The BBOP, located at the Lawrence Berkeley National Labs, is a diverse group of scientific researchers and software engineers dedicated to developing tools and applying computational technologies to solve biological problems. Members of the group contribute to a number of projects, including the Gene Ontology, OBO Foundry, the Phenotypic Quality Ontology, modENCODE, and the Generic Model Organism Database Project. Our group is focused on the development, use, and integration of ontolgies into biological data analysis. Software written or maintained by BBOP is accessible through the site.

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Cite this (Berkeley Drosophila Genome Project, RRID:SCR_013094)

URL: http://www.fruitfly.org

Resource Type: Resource, topical portal, production service resource, analysis service resource, database, data analysis service, narrative resource, experimental protocol, portal, service resource, material resource, data or information resource

Database on the sequence of the euchromatic genome of Drosophila melanogaster In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community. Resources * Universal Proteomics Resource: Search for clones for expression and tissue culture * Materials: Request genomic or cDNA clones, library filters or fly stocks * Download Sequence data sets and annotations in fasta or xml format by http or ftp * Publications: Browse or download BDGP papers * Methods: BDGP laboratory protocols and vector maps * Analysis Tools: Search sequences for CRMs, promoters, splice sites, and gene predictions * Apollo: Genome annotation viewer and editor September 15, 2009 Illumina RNA-Seq data from 30 developmental time points of D. melanogaster has been submitted to the Short Read Archive at NCBI as part of the modENCODE project. The data set currently contains 2.2 billion single-end and paired reads and over 201 billion base pairs.

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Cite this (Bioconductor, RRID:SCR_006442)

URL: http://www.bioconductor.org/

Resource Type: Resource, catalog, data or information resource, database

A catalog of tools and software packages for the analysis and comprehension of high-throughput genomic data that uses the R statistical programming language. Bioconductor has a development version to which new features and packages are added prior to incorporation in the release. A large number of meta-data packages provide pathway, organism, microarray and other annotations. The broad goals of the Bioconductor project are: to provide widespread access to a broad range of powerful statistical and graphical methods for the analysis of genomic data; to facilitate the inclusion of biological metadata in the analysis of genomic data; to provide a common software platform that enables the rapid development and deployment of extensible, scalable, and interoperable software; and to train researchers on computational and statistical methods for the analysis of genomic data.

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Cite this (Bio-eagle, RRID:SCR_015991)

URL: https://data.broadinstitute.org/alkesgroup/Eagle/

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

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

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    BioGRID

Cite this (BioGRID, RRID:SCR_007393)

URL: http://www.thebiogrid.org/

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

A curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts. The current version searches over 41,000 publications containing over 720,000 interactions (June 2014) and contributions are welcome. Complete coverage of the entire literature is maintained for budding yeast (S. cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. It provides interaction data to several model organism databases, resources such as Entrez-Gene, SGD, TAIR, FlyBase and other interaction meta-databases. The entire BioGRID 3.0 data collection may be downloaded in multiple file formats, including IMEx compatible PSI MI XML. For developers, BioGRID interactions are also available via a REST based Web Service and Cytoscape plugin.

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    BioPerl

Cite this (BioPerl, RRID:SCR_002989)

URL: http://www.bioperl.org

Resource Type: Resource, wiki, source code, narrative resource, software repository, software resource, software toolkit, data or information resource

BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

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