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https://kona.nhgri.nih.gov/mnemiopsis/
Portal to obtain genomic information on Mnemiopsis. Data available provide annotations and other key biological information not available elsewhere. Used to advance research projects aimed at understanding phylogenetic diversity and evolution of proteins that play fundamental role in metazoan development. Collection of sequenced, assembled, annotated, and performed preliminary analysis of genome of Mnemiopsis.
Proper citation: Mnemiopsis Genome Project Portal (RRID:SCR_018293) Copy
https://code.google.com/p/ontology-for-genetic-interval/
An ontology that formalized the genomic element by defining an upper class genetic interval using BFO as its framework. The definition of genetic interval is the spatial continuous physical entity which contains ordered genomic sets (DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence structure.
Proper citation: Ontology for Genetic Interval (RRID:SCR_003423) Copy
http://dunham.gs.washington.edu/protocols.shtml
A portal for Maitreya Dunham's lab, which works on the genomic analysis of experimental evolution in yeast using microarrays and the chemostat. Research interests of the lab include experimental evolution of genetic networks in yeast, aneuploidy and copy number variation, comparative genomics, technology development and human genetics in yeast.
Proper citation: Maitreya Dunham's Lab (RRID:SCR_000784) Copy
http://atlasgeneticsoncology.org/
Online journal and database devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases. Its aim is to cover the entire field under study and it presents concise and updated reviews (cards) or longer texts (deep insights) concerning topics in cancer research and genomics.
Proper citation: Atlas of Genetics and Cytogenetics in Oncology and Haematology (RRID:SCR_007199) Copy
https://github.com/esctrionsit/snphub
Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data.
Proper citation: SnpHub (RRID:SCR_018177) Copy
http://www.imperial.ac.uk/research/animallectins
Resource presents information about animal lectins involved in various sugar recognition processes.
Proper citation: genomics resource for animal lectins (RRID:SCR_018122) Copy
http://smd.stanford.edu/cgi-bin/source/sourceSearch
SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool
Proper citation: SOURCE (RRID:SCR_005799) Copy
https://genomecenter.ucdavis.edu/core-facilities/
Genome Center uses technologies to understand how heritable genetic information of diverse organisms functions in health and disease. Provides research facilities, service cores, and staff for genomics research and training. Core facilities for Bioinformatics,DNA Technologies and Expression Analysis, Metabolomics, Proteomics,TILLING Core,Yeast One Hybrid Services Core.
Proper citation: UC Davis Genome Center Labs and Facilities (RRID:SCR_012480) Copy
http://www.daimi.au.dk/%7Emailund/SNPFile/
Software library and API for manipulating large SNP datasets with associated meta-data, such as marker names, marker locations, individuals'' phenotypes, etc. in an I/O efficient binary file format. In its core, SNPFile assumes very little about the metadata associated with markers and individuals, but leaves this up to application program protocols. (entry from Genetic Analysis Software)
Proper citation: SNPFILE (RRID:SCR_009402) Copy
https://atgu.mgh.harvard.edu/plinkseq/
An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software)
Proper citation: PLINK/SEQ (RRID:SCR_013193) Copy
http://disulfind.dsi.unifi.it/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, 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.
Proper citation: DISULFIND (RRID:SCR_016072) Copy
https://github.com/osallou/cassiopee-c
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.
Proper citation: Cassiopee (RRID:SCR_016056) Copy
Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility.
Proper citation: NeMOarchive (RRID:SCR_016152) Copy
http://genome.imim.es/software/gfftools/GFF2APLOT.html
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.
Proper citation: Gff2aplot (RRID:SCR_016128) Copy
http://ssadedin.github.io/ximmer/
Software to help users of targeted high throughput genomic sequencing data to accurately detect copy number variants (CNVs). Framework for running and evaluating other copy number detection tools.Used for evaluating and improving performance of CNV detection in exome and targeted sequencing data.
Proper citation: Ximmer (RRID:SCR_016427) Copy
Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis.
Proper citation: GOTrack (RRID:SCR_016399) Copy
https://genome.jgi.doe.gov/programs/fungi/1000fungalgenomes.jsf
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.
Proper citation: 1000 Fungal Genome Project (RRID:SCR_016463) Copy
Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information.
Proper citation: Global Catalogue of Microorganisms (RRID:SCR_016460) Copy
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.
Proper citation: CajaDB (RRID:SCR_016506) Copy
Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information.
Proper citation: PaVE (RRID:SCR_016599) Copy
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