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on page 1 showing 20 out of 61 results

Cite this (1000 Fungal Genome Project, RRID:SCR_016463)

URL: https://genome.jgi.doe.gov/programs/fungi/1000fungalgenomes.jsf

Resource Type: Resource, topical portal, data access protocol, database, web service, organism-related portal, portal, software resource, project portal, data or information resource

Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment.

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Cite this (Allen Brain Atlas, RRID:SCR_017001)

URL: http://portal.brain-map.org/

Resource Type: Resource, atlas, project portal, portal, data or information resource

Projects within the Allen Institute for Brain Science for creating Mouse and Human Brain atlases. Combine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases.

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Cite this (Allen Human Brain Atlas, RRID:SCR_007416)

URL: http://human.brain-map.org/

Resource Type: Resource, data processing software, database, software application, data visualization software, software resource, atlas, data or information resource

Multi modal atlas of human brain that integrates anatomic and genomic information, coupled with a suite of visualization and mining tools to create an open public resource for brain researchers and other scientists. Data include magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), histology and gene expression data derived from both microarray and in situ hybridization (ISH) approaches. Brain Explorer 2 is a desktop software application for viewing the human brain anatomy and gene expression data in 3D. It is available for download.

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    Arvados

Cite this (Arvados, RRID:SCR_002223)

URL: https://arvados.org/

Resource Type: Resource, service resource, data repository, storage service resource

A free and open source bioinformatics platform for storing, organizing, processing, and sharing genomic and other biomedical big data. The platform is designed to make it easier for bioinformaticians to develop analyses, developers to create genomic web applications and IT administers to manage large-scale compute and storage genomic resources. The platform is designed to run on top of cloud operating systems such as Amazon Web Services and OpenStack. Currently, there are implementations that work on AWS and Xen+Debian/Ubuntu. Functionally, Arvados has two major sets of capabilities: (a) data management and (b) compute management.

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    ASPGD

Cite this (ASPGD, RRID:SCR_002047)

URL: http://www.aspgd.org/

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

Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions.

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    Augustus

Cite this (Augustus, RRID:SCR_008417)

URL: http://bioinf.uni-greifswald.de/augustus/

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

Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes.

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    BEAGLE

Cite this (BEAGLE, RRID:SCR_001789)

URL: http://faculty.washington.edu/browning/beagle/beagle.html

Resource Type: Resource, software resource, software application

Software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can * phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios. * infer sporadic missing genotype data. * impute ungenotyped markers that have been genotyped in a reference panel. * perform single marker and haplotypic association analysis. * detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals. Beagle can also be used in conjunction with PRESTO, a program for fast and flexible permutation testing. PRESTO can compute empirical distributions of order statistics, analyze stratified data, and determine significance levels for one-stage and two-stage genetic association studies. BEAGLE is written in Java and runs on any computing platform with a Java version 1.6 interpreter (e.g. Windows, Unix, Linux, Solaris, Mac).

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Cite this (Bioconductor, RRID:SCR_006442)

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

Resource Type: Resource, data analysis software, data processing software, software library, database, software application, software repository, catalog, software resource, software toolkit, data or information resource

Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.

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    Blixem

Cite this (Blixem, RRID:SCR_015994)

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 sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites.

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    BOOST

Cite this (BOOST, RRID:SCR_013133)

URL: http://bioinformatics.ust.hk/BOOST.html

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

Software application (entry from Genetic Analysis Software) for a method for detecting gene-gene interactions. It allows examining all pairwise interactions in genome-wide case-control studies.

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    CajaDB

Cite this (CajaDB, RRID:SCR_016506)

URL: http://cajadb.neuro.ufrn.br

Resource Type: Resource, software resource, web application, data or information resource, database

Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network.

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Cite this (Cassiopee, RRID:SCR_016056)

URL: https://github.com/osallou/cassiopee-c

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

Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity.

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Cite this (ComplexHeatmap, RRID:SCR_017270)

URL: https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html

Resource Type: Resource, data visualization software, software application, data analysis software, data processing software, software resource

Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns.

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    DETONATE

Cite this (DETONATE, RRID:SCR_017035)

URL: http://deweylab.biostat.wisc.edu/detonate/

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

Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences.

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Cite this (DISULFIND, RRID:SCR_016072)

URL: http://disulfind.dsi.unifi.it/

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

Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks.

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    Entrez

Cite this (Entrez, RRID:SCR_016640)

URL: https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html

Resource Type: Resource, web service, software resource, portal, data access protocol, data or information resource

Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references.
Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ.

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Cite this (Eutherian comparative genomic analysis protocol, RRID:SCR_014401)

URL: http://www.sciencedirect.com/science/article/pii/S2352340915003510

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

Public eutherian reference genomic sequence data sets ushered in new era in biology and medicine. Nevertheless, future updates and revisions of eutherian gene data sets were expected, due to incompleteness of reference genomic sequence assemblies and potential genomic sequence errors.

The open science research project "Comparative genomic analysis of eutherian genes" established eutherian comparative genomic analysis protocol RRID:SCR_014401 as one framework of updates and revisions of eutherian gene data sets. The protocol included gene annotations, phylogenetic analysis and protein molecular evolution analysis, as well as new test of reliability of public eutherian genomic sequences using genomic sequence redundancies and new test of protein molecular evolution using relative synonymous codon usage statistics.

The protocol was applicable in updates and revisions of 11 major eutherian gene data sets, including 1504 complete coding sequences deposited in European Nucleotide Archive as curated third party data gene data sets under accession numbers: FR734011-FR734074, HF564658-HF564785, HF564786-HF564815, HG328835-HG329089, HG426065-HG426183, HG931734-HG931849, LM644135-LM644234, LN874312-LN874522, LT548096-LT548244, LT631550-LT631670 and LT962964-LT963174. In addition, the protocol curated other eutherian gene data sets (data in preparation).

OPEN SCIENCE RESEARCH PROJECT: COMPARATIVE GENOMIC ANALYSIS OF EUTHERIAN GENES
PROJECT LEADER: Marko Premzl PhD, The Australian National University Alumni, 4 Kninski trg Sq., Zagreb, Croatia
E-MAIL CONTACT ADDRESS: Marko.Premzl@alumni.anu.edu.au
NCBI SciENcv: https://www.ncbi.nlm.nih.gov/myncbi/mpremzl/cv/130205/
Open Science Framework Projects: https://osf.io/ax3ts/

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Cite this (GenomicFeatures, RRID:SCR_016960)

URL: http://bioconductor.org/packages/GenomicFeatures/

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

Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.

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Cite this (Genomic Ranges, RRID:SCR_017051)

URL: http://bioconductor.org/packages/GenomicRanges/

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

Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome.

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Cite this (Gff2aplot, RRID:SCR_016128)

URL: http://genome.imim.es/software/gfftools/GFF2APLOT.html

Resource Type: Resource, data visualization software, software application, data processing software, software resource

Software application to visualize the alignment of two genomic sequences together with their annotations. Used to generate print-quality images for comparative genome sequence analysis.

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