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http://cell-innovation.nig.ac.jp/maser/AllPipelines/P000001138_en.html

Software pipeline that visualizes mapping results (in BAM format) on Genome Explorer.

Proper citation: loadBAM2ge_db (RRID:SCR_015951) Copy   

•   Source: SciCrunch Registry

https://blobtoolkit.genomehubs.org/blobtools2/

Software suite for identifying and isolating non-target data in draft and publicly available genome assemblies. Used to process assembly, read and analysis files for fully reproducible interactive exploration in browser-based Viewer. Used for interactive quality assessment of genome assemblies .BlobTools2 is reimplementation of BlobTools, written in Python 3 with fully modular design to make creating new datasets and adding additional analysis types easier.

Proper citation: BlobTools2 (RRID:SCR_023351) Copy   

•   Source: SciCrunch Registry

https://chordate.bpni.bio.keio.ac.jp/chordate/faba/1.4/top.html

Image resource including ascidian's three-dimensional (3D) and cross-sectional images through the developmental time course. These images were reconstructed from more than 3,000 high-resolution real images collected by confocal laser scanning microscopy (CLSM) at newly defined 26 distinct developmental stages (stages 1-26) from fertilized egg to hatching larva, which were grouped into six periods named the zygote, cleavage, gastrula, neurula, tailbud, and larva periods. The data set will be helpful in standardizing developmental stages for morphology comparison as well as for providing guidelines for several functional studies of a body plan in chordate.

Proper citation: Four-dimensional Ascidian Body Atlas (RRID:SCR_001691) Copy   

•   Source: SciCrunch Registry

http://www.worm.mpi-cbg.de/phenobank/cgi-bin/ProjectInfoPage.py

A database that provides primary data from two high-content screens that profile the set of ~900 essential C. elegans genes (~5% of the genome) required for embryo production and/or events during the first two embryonic divisions. Phenobank houses the movies, scored defects, and phenotypic classification data for the embryo-filming and gonad morphology screens.

Proper citation: PhenoBank (RRID:SCR_000930) Copy   

•   Source: SciCrunch Registry

http://igenbio.com/

A web-based genome analysis platform that integrates proprietary functional genomic data, metabolic reconstructions, expression profiling, and biochemical and microbiological data with publicly available information. Focused on microbial genomics, it provides better and faster identification of gene function across all organisms. Building upon a comprehensive genomic database integrated with a collection of microbial metabolic and non-metabolic pathways and using proprietary algorithms, it assigns functions to genes, integrates genes into pathways, and identifies previously unknown or mischaracterized genes, cryptic pathways and gene products. . * Automated and manual annotation of genes and genomes * Analysis of metabolic and non-metabolic pathways to understand organism physiology * Comparison of multiple genomes to identify shared and unique features and SNPs * Functional analysis of gene expression microarray data * Data-mining for target gene discovery * In silico metabolic engineering and strain improvement

Proper citation: ERGO (RRID:SCR_001243) Copy   

•   Source: SciCrunch Registry

http://dire.dcode.org

Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data.

Proper citation: Distant Regulatory Elements (RRID:SCR_003058) Copy   

•   Source: SciCrunch Registry

http://hgc.rockefeller.edu/

An interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways.

Proper citation: Human Gene Connectome Server (RRID:SCR_002627) Copy   

•   Source: SciCrunch Registry

http://www.labspaces.net/DNA

Hi. I''m genegeek (aka Catherine Anderson). I realized during my PostDoc that I preferred learning and explaining new results to doing science so I started a non-traditional career of teaching and outreach. I''ll be using this space to explore public perception of genetics and other cool molecular biology stuff. I hope to add to the great discussions re: new science discoveries and general understanding of genetics. I''ve been running an outreach program and enjoy talking to non-experts about their opinions and understanding. I hope my enthusiasm for the topics can come through the screen. My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

Proper citation: Daring Nucleic Adventures - genegeek (RRID:SCR_005215) Copy   

•   Source: SciCrunch Registry

http://gst.ornl.gov/

We are the Computational Biology and Bioinformatics Group of the Biosciences Division of Oak Ridge National Laboratory. We conduct genetics research and system development in genomic sequencing, computational genome analysis, and computational protein structure analysis. We provide bioinformatics and analytic services and resources to collaborators, predict prospective gene and protein models for analysis, provide user services for the general community, including computer-annotated genomes in Genome Channel. Our collaborators include the Joint Genome Institute, ORNL''s Computer Science and Mathematics Division, the Tennessee Mouse Genome Consortium, the Joint Institute for Biological Sciences, and ORNL''s Genome Science and Technology Graduate Program.

Proper citation: Computational Biology at ORNL (RRID:SCR_005710) Copy   

•   Source: SciCrunch Registry

http://www.compbio.dundee.ac.uk/gotcha/gotcha.php

GOtcha provides a prediction of a set of GO terms that can be associated with a given query sequence. Each term is scored independently and the scores calibrated against reference searches to give an accurate percentage likelihood of correctness. These results can be displayed graphically. Why is GOtcha different to what is already out there and why should you be using it? * GOtcha uses a method where it combines information from many search hits, up to and including E-values that are normally discarded. This gives much better sensitivity than other methods. * GOtcha provides a score for each individual term, not just the leaf term or branch. This allows the discrimination between confident assignments that one would find at a more general level and the more specific terms that one would have lower confidence in. * The scores GOtcha provides are calibrated to give a real estimate of correctness. This is expressed as a percentage, giving a result that non-experts are comfortable in interpreting. * GOtcha provides graphical output that gives an overview of the confidence in, or potential alternatives for, particular GO term assignments. The tool is currently web-based; contact David Martin for details of the standalone version. Platform: Online tool

Proper citation: GOtcha (RRID:SCR_005790) Copy   

•   Source: SciCrunch Registry

http://tabit.ucsd.edu/sdec/

A next-generation web-based application that aims to provide an integrated solution for both visualization and analysis of deep-sequencing data, along with simple access to public datasets.

Proper citation: Systems Transcriptional Activity Reconstruction (RRID:SCR_005622) Copy   

•   Source: SciCrunch Registry

http://igs-server.cnrs-mrs.fr/mgdb/Rickettsia/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. Rickettsia are obligate intracellular bacteria living in arthropods. They occasionally cause diseases in humans. To understand their pathogenicity, physiologies and evolutionary mechanisms, RicBase is sequencing different species of Rickettsia. Up to now we have determined the genome sequences of R. conorii, R. felis, R. bellii, R. africae, and R. massiliae. The RicBase aims to organize the genomic data to assist followup studies of Rickettsia. This website contains information on R. conorii and R. prowazekii. A R. conorii and R. prowazekii comparative genome map is also available. Images of genome maps, dendrogram, and sequence alignment allow users to gain a visualization of the diagrams.

Proper citation: Rickettsia Genome Database (RRID:SCR_007102) Copy   

•   Source: SciCrunch Registry

http://www.dnastar.com/t-genvision.aspx

A genomic visualization application to support easy generation of publication quality graphics and maps. It produces high quality images of annotated genomes but it can also be customized to accentuate specific areas of interest, such as comparing gene functionality, illustrating gene expression levels, and visualizing the coverage in an assembled contig.

Proper citation: GenVision (RRID:SCR_001166) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/genomes

The EBI genomes pages give access to a large number of complete genomes including bacteria, archaea, viruses, phages, plasmids, viroids and eukaryotes. Methods using whole genome shotgun data are used to gain a large amount of genome coverage for an organism. WGS data for a growing number of organisms are being submitted to DDBJ/EMBL/GenBank. Genome entries have been listed in their appropriate category which may be browsed using the website navigation tool bar on the left. While organelles are all listed in a separate category, any from Eukaryota with chromosome entries are also listed in the Eukaryota page. Within each page, entries are grouped and sorted at the species level with links to the taxonomy page for that species separating each group. Within each species, entries whose source organism has been categorized further are grouped and numbered accordingly. Links are made to: * taxonomy * complete EMBL flatfile * CON files * lists of CON segments * Project * Proteomes pages * FASTA file of Proteins * list of Proteins

Proper citation: EBI Genomes (RRID:SCR_002426) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.udel.edu/Research/skategenomeproject

Core facility provides a model for collaborative approaches to use specialized resources and expertise in an integrated process. Core builds on the expertise and resources provided by the Bioinformatics Cores of the five northeastern states that form NECC. The Skate Genome Annotation Workshops and Jamborees offer training and opportunities for faculty and students to work with and annotate genome sequences. Workshops include lectures, tutorials and exercises annotating the genome of the little skate, Leucoraja erinacea.

Proper citation: University of Delaware Skate Genome Project (RRID:SCR_005300) Copy   

•   Source: SciCrunch Registry

http://www.broad.mit.edu/annotation/fungi/fgi/

Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics.

Proper citation: Fungal Genome Initiative (RRID:SCR_003169) Copy   

•   Source: SciCrunch Registry

http://aws.amazon.com/1000genomes/

A dataset containing the full genomic sequence of 1,700 individuals, freely available for research use. The 1000 Genomes Project is an international research effort coordinated by a consortium of 75 companies and organizations to establish the most detailed catalogue of human genetic variation. The project has grown to 200 terabytes of genomic data including DNA sequenced from more than 1,700 individuals that researchers can now access on AWS for use in disease research free of charge. The dataset containing the full genomic sequence of 1,700 individuals is now available to all via Amazon S3. The data can be found at: http://s3.amazonaws.com/1000genomes The 1000 Genomes Project aims to include the genomes of more than 2,662 individuals from 26 populations around the world, and the NIH will continue to add the remaining genome samples to the data collection this year. Public Data Sets on AWS provide a centralized repository of public data hosted on Amazon Simple Storage Service (Amazon S3). The data can be seamlessly accessed from AWS services such Amazon Elastic Compute Cloud (Amazon EC2) and Amazon Elastic MapReduce (Amazon EMR), which provide organizations with the highly scalable compute resources needed to take advantage of these large data collections. AWS is storing the public data sets at no charge to the community. Researchers pay only for the additional AWS resources they need for further processing or analysis of the data. All 200 TB of the latest 1000 Genomes Project data is available in a publicly available Amazon S3 bucket. You can access the data via simple HTTP requests, or take advantage of the AWS SDKs in languages such as Ruby, Java, Python, .NET and PHP. Researchers can use the Amazon EC2 utility computing service to dive into this data without the usual capital investment required to work with data at this scale. AWS also provides a number of orchestration and automation services to help teams make their research available to others to remix and reuse. Making the data available via a bucket in Amazon S3 also means that customers can crunch the information using Hadoop via Amazon Elastic MapReduce, and take advantage of the growing collection of tools for running bioinformatics job flows, such as CloudBurst and Crossbow.

Proper citation: 1000 Genomes Project and AWS (RRID:SCR_008801) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/Projects/Fungi/

Fungal genomes available from the Sanger Institute. Data are accessible in a number of ways; for each organism there is a BLAST server, allowing search of the sequences. Sequences can also be down-loaded directly by FTP. In addition, for those organisms being sequenced using a cosmid approach, finished and annotated cosmids are submitted to EMBL and other public databases.

Proper citation: Fungi Sequencing Projects (RRID:SCR_008524) Copy   

•   Source: SciCrunch Registry

https://www.encodeproject.org/

Consortium to build comprehensive parts list of functional elements in human genome. This includes elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Data from 2012-present.

Proper citation: Encode (RRID:SCR_015482) Copy   

•   Source: SciCrunch Registry

http://www.iu.edu/~beca/

Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version.

Proper citation: BECA (RRID:SCR_015846) Copy   

•   Source: SciCrunch Registry