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Anolis carolinensis
A database which offers gene annotation of Anolis carolinensis also known as Carolina anole an arboreal lizard. The anole lizard genome is composed of 13 chromosomes, assembled from 41.9861 contigs and 2.143 scaffolds. The total number of bases in the genome is 1.78Gb. The gene set for anole lizard was built using the Ensembl genebuild pipeline. In addition to the main set, gene models have been predicted for each tissue type using the RNA-Seq pipeline. Anolis carolinensis belongs to the Dactyloidae family.
EuMicrobedbLite
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A light weight comprehensive genome resource and sequence analysis platform for oomycete organisms. EuMicrobedbLite is a successor of the VBI Microbial Database (VMD) that was built using the Genome Unified Schema (GUS). This database has 26 publicly available genomes and 10 EST datasets of oomycete organisms. The browser page has dynamic tracks presenting comparative genomics analyses, coding and non-coding data, tRNA genes, repeats and EST alignments. In addition, 44777 core conserved proteins were defined from twelve oomycete organisms that form 2974 clusters. The user interface has undergone major changes for ease of browsing. Queryable comparative genomics information, conserved orthologous genes and pathways are among the new key features updated in this database. Annotations for the organisms are updated once every six months to ensure quality.
CyanoBase
Provides an easy way of accessing the sequences and all-inclusive annotation data on the structures of the cyanobacterial genomes. It contains cyanobacterial genomic sequences from 376 species, which consist of 86 complete and 290 draft genomes. The user interface was optimized for large genomic data to include the use of semantic web technologies and JBrowse. CyanoBase focuses on the representation and reusability of reference genome annotations, which are continuously updated by manual curation. Advanced users can also retrieve this information through the representational state transfer-based web application programming interface in an automated manner.
MBGD / Microbial Genome Database
Gathers information related to full microbial genomes. MBGD is a repository that focuses in assisting researchers in comparing genomic information by providing data about both prokaryotic and eukaryotic microbes as well as four multicellular eukaryotes. The database contains precomputed orthologs tables and permits users to generate their own. It also includes a function: MyMBGD, for submitting users’ data to the server and perform a customized ortholog analysis.
Pseudomonas Genome Database
Collaborates with an international panel of expert Pseudomonas researchers to provide high quality updates to the PAO1 genome annotation and make cutting edge genome analysis data available. The Pseudomonas Genome Database integrates completely-sequenced Pseudomonas genome sequences and their annotations with genome-scale, high-precision computational predictions and manually curated annotation updates. The wide range of tools for comparing Pseudomonas annotations and sequences includes a strain-specific access point for viewing high precision computational predictions including updated, more accurate, protein subcellular localization and genomic island predictions.
Nematode.net
Consists of a community resource dedicated to the study of parasitic nematodes. Nematode.net is a publicly available resource that provides access to annotation of genomes, expression and related genome-scale data, as well as data-mining tools and their comparative data products. NemaGene hosts annotation for almost 1.1 million genes and transcripts spanning 67 nematode species and NemaBrowse allows displaying of SnpEff-annotated variants from isolates with different phenotypes. The database is a part of Helminth.net, an evolving collection of databases hosting resources for helminths.
PGSB PlantsDB / Plant Genome and Systems Biology PlantsDB
A database framework for the comparative analysis and visualization of plant genome data. PGSB PlantsDB has been updated with new data sets and types as well as specialized tools and interfaces to address user demands for intuitive access to complex plant genome data. It is part of the EU-funded transPLANT network which facilitates the exchange, integration and virtual aggregation of plant genome data from distributed resources as well as the development of common standards and protocols.
GenColors
Aims to facilitate presentation of bacterial genomes, as well as annotation and analysis. GenColors is a web-based software/database system that provides tools for visualizing, comparing and analyzing the data. It consists in an approach with special emphasis on the comparison of closely related bacterial or small eukaryote genomes including the option of homology-based gene annotation. The software allows users to apply comparative genome analysis tools to a set of related genomes.
GreenPhylDB
Provides a database for comparative genomic analysis full genomes. GreenPhylDB is a web accessible, user-friendly comparative platform for plant genomes studies including family classification, phylogenomic analysis information and cross-reference links. It comes with a set of dedicated tools, InterPro, KEGG, TAIR or sequences ID as queries. It also integrates a dedicated phylogenomics tool, GreenPhyl Ortholog Search Tool (GOST), to search orthologs using protein sequences from other plant species.
OryGenesDB
A search database for rice reverse genetics. OryGenesDB contains flanking sequence tags of various mutagens and functional genomics data, collected from both international insertion collections and the literature. OryGenesDB is also a user-oriented web application that automates and organizes web queries in rice functional genomics. Users can run their queries and store the output and update the results as the source databases are continuously independently updated. OryGenesDB offers a way to accelerate the manual process of integrating and compiling data from heterogeneous sources.
LegumeIP
Hosts large-scale genomics and transcriptomics data and provides integrative bioinformatics tools for the study of gene function and evolution in legumes. Our recent updates in LegumeIP 2.0 include gene and protein sequences, gene models and annotations, syntenic regions, protein families and phylogenetic trees for six legume species: Medicago truncatula, Glycine max (soybean), Lotus japonicus, Phaseolus vulgaris (common bean), Cicer arietinum (chickpea) and Cajanus cajan (pigeon pea) and two outgroup reference species: Arabidopsis thaliana and Poplar trichocarpa. All expression profiles were manually curated, annotated using free text descriptions, keywords and further hierarchically organized following the Experimental Ontology (EO) and Plant Ontology (PO), allowing users to browse, search and retrieve gene expression profiles for the experiments of their choice using both the EO tree view browser and comprehensive keyword searches. This integrative gene atlas is essential and extremely valuable for the study of gene function and provide valuable large-scale gene expression data to biologists through user-friendly web interfaces.
Phytozome
Provides a centralized hub for plant genome and gene family data and analysis. Phytozome is a comparative hub which provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization and gives access to the sequences and functional annotations of complete plant genomes, including all the land plants and selected algae. The platform provides comparative genomics tools that help to link model systems with other plants of economic and ecological importance.
HGTree
Provides pre-calculated horizontal gene transfer (HGT) events in prokaryotic genomes (Archaea and Bacteria). HGTree defines lateral gene transfer by comparing the gene tree for each orthologous gene set to the reference species tree. Conflict between gene and species trees is taken as indication of non-vertical evolution (including HGT and convergence) and is displayed graphically for quick understanding. It also provides four types of HGT analysis options. The database can facilitate the understand of microbial taxonomy and evolution.
Macropus eugenii
Offers gene annotation of Macropus eugenii also known as tammar wallaby. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. For the contigs in the assembly the N50 size is 2.5 kb and for the scaffolds 14.5 kb. The total length of all of the contigs in the assembly is 2.55 Gb with the assembly spanning 2.78 Gb. The gene set for wallaby contains a total of 17,877 genes, of which 15,290 are protein coding. Macropus eugenii belongs to the Macropodidae family.
Helminth.net
Provides access to integrated data and tools for helminths undergoing targeted active research studies. Helminth.net is an evolving collection of databases hosting resources for helminths, which includes roundworms (Nematoda with Nematode.net) and flatworms (Platyhelminthes with Trematode.net). It provides comprehensive functional gene/protein annotation, stage and tissue specific expression information, population-based variant annotation, ChEMBL drug target association and interactive tools for performing complex multi-factor searches and analyzes.
LEGER
Supports functional Listeria genome analyses by combining information obtained by applying bioinformatics methods and from public databases to improve the original annotations. LEGER offers three unique key features: (i) it is the first comprehensive information system focusing on the functional assignment of genes and proteins; (ii) integrated visualization tools, KEGG pathway and Genome Viewer, alleviate the functional exploration of complex data; and (iii) LEGER presents results of systematic post-genome studies, thus facilitating analyses combining computational and experimental results.
Xenbase
Integrates variety of data from biomedical model genus and archives large data sets that would otherwise be unavailable to the global scientific community. Researchers can easily navigate from genome content to gene page reports, literature, experimental reagents and many other features using hyperlinks. Xenbase has been designed to facilitate direct comparison of information from Xenopus genes with their human orthologs. Search returns will show all gene pages on which the OMIM entry is linked, and all other OMIM disease associations for that gene.
PlanMine
Aims to provide an easily accessible and minable repository of general planarian sequence data. Our dual mission objective is to first, provide opportunities for comparing and mining planarian transcriptomes and RNA-Seq data sets created across the community; second, to catalyze the comparative analysis of the phenotypic diversity amongst planarian species. We chose the popular InterMine data warehouse system for PlanMine in order to facilitate comparisons with other model systems and to make the fascinating biology of planarians accessible to the general life sciences research community.
Comparasite
Contains full-length cDNA sequence data. Comparasite is an integrated database consisting of seven sub-databases of apicomplexa protozoa (Plasmodium falciparum, Plasmodium yoelii, Plasmodium vivax, Plasmodium berghei, Toxoplasma gondii, Cryptosporidium parvum) and a tapeworm, (Echinococcus multilocularis). The database provides base not only for analyzing gene functions of individual species in a concrete and versatile ways but also for understanding the biological concepts of parasitism in a more abstract way.
InsectBase
Provides a comprehensive platform for researchers who have interests in analyzing insect genes. InsectBase contains more than 12 millions of sequences, encompassing the genomes of 138 insects, transcriptomes of 116 insects, gene sets of 61 insects, 36 gene families of 60 insects, 7,544 miRNAs of 69 insects, 96,925 piRNAs from two insects, 22,536 pathways of 78 insects, 679,881 untranslated regions (UTR) of 84 insects and 160,905 coding sequences (CDS) of 74 insects. Besides offering widely used Web-services such as a search tool, BLAST and GBrowse, InsectBase is also a platform for comparative genomics analysis on gene families, pathways and orthologs. Additionally, iFacebook is designed to provide a Facebook-like social network for the insect community by constructing relationships between researchers, genes and insect species.
MyMpn
An online resource devoted to studying the human pathogen Mycoplasma pneumoniae, a minimal bacterium causing lower respiratory tract infections. MyMpn hosts a wealth of omics-scale datasets generated by hundreds of experimental and computational analyses. These include data obtained from gene expression profiling experiments, gene essentiality studies, protein abundance profiling, protein complex analysis, metabolic reactions and network modeling, cell growth experiments, comparative genomics and 3D tomography.
VigGS / Vigna Genome Server
A genome database of the genus Vigna based on the recently sequenced azuki bean genome, which incorporates annotated exon-intron structures, along with evidence for transcripts and proteins, visualized in GBrowse. VigGS also facilitates user construction of multiple alignments between azuki bean genes and those of six related dicot species. In addition, the database displays sequence polymorphisms between azuki bean and its wild relatives and enables users to design primer sequences targeting any variant site. VigGS offers a simple keyword search in addition to sequence similarity searches using BLAST and BLAT. To incorporate up to date genomic information, VigGS automatically receives newly deposited mRNA sequences of pre-set species from the public database once a week. Users can refer to not only gene structures mapped on the azuki bean genome on GBrowse but also relevant literature of the genes. VigGS plays a central role as a knowledge base for genomic and genetic studies of Vigna and other legume species.
Cyanidioschyzon merolae
A database offering the genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae. This project presents the complete sequence of 16,546,747 nucleotides covering 100% of the 20 linear chromosomes from telomere to telomere, representing the simple and unique chromosomal structures of the eukaryotic cell. The C. merolae genome contains the smallest known histone-gene cluster, a unique telomeric repeat for all chromosomal ends, and an extremely low number of transposons. It belongs to the Cyanidiaceae family.
OXGRID / The Oxford Grid Project
Provides access to zoomable and annotated web-based Oxford grids. OXGRID is a database allowing users to browse comparative mapping data. The multiple cells view contains a grid of cells representing pairwise comparisons for each of the possible linkage group combinations and provides an overview of the comparative map. A mouse click over a selected cell launches a detailed view. The OxfordGrid software for generating an interactive Oxford grid is downloadable on the website.
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