The major principles of comparative genomics are straightforward. Common features of two organisms will often be encoded within the DNA that is conserved between the species. More precisely, the DNA sequences encoding the proteins and RNAs responsible for functions that were conserved from the last common ancestor should be preserved in contemporary genome sequences. Likewise, the DNA sequences controlling the expression of genes that are regulated similarly in two related species should also be conserved. Conversely, sequences that encode (or control the expression of) proteins and RNAs responsible for differences between species will themselves be divergent.
Consists of a genome resource and sequence analysis platform for oomycete organisms. The EuMicrobedbLite system includes different assembly versions, annotations and the nomenclature of the features. This platform works conjointly with different programs and provides a solution to run a variety of sequence analysis programs. Moreover, the data visualization interface of the database has five major components, namely genome browser, gene detail page, genome synteny page, query page and toolkit page.
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.
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.
Allows users to query, visualize, analyze, and compare plant genome and pathway data across crops and model species. Gramene is a resource that uses information generated from projects supported by public funds to improve the study of cross-species comparisons. The database provides a search interface, and views and functionalities for Plant Reactome. It also shares infrastructure, specialized software components and pre-computed data with Ensembl Plants.
Consists of a community resource dedicated to the study of parasitic nematodes. Nematode.net provides access to annotation of genomes, expression and related genome-scale data, as well as data-mining tools and their comparative data products. It hosts annotation for more than 1 million genes and transcripts. It includes a module, NemaBrowse, that allows the 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.
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.
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.
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.
Offers users a platform for browsing different comparative genomic analyses in four different phyla: Plants, non-vertebrate Metazoans, Fungi, and Vertebrate. Genomicus is an online resource that allows researchers to analyze or explore genomic information from extant species. This database enables comparison between unlimited numbers of genomes and provides comprehensive overview of gene and genome organization between modern species.
Provides a data source of fungal genomics. CFGP stores more 280 genomes corresponding to more than 150 fungal and Oomycete species as well as up to 200 genomes of bacteria, plants and animals. It proposes several functions like searching homologous genes to queries in multiple species simultaneously, querying genomes according to their taxonomic positions or displaying presentation of diverse genomic context.
Gathers intra- or interplant genome alignment information. PGDD enables the identification and the cataloging of plant genes in terms of intragenome or cross-genome syntenic relationships. This public database contains data for several plant species including bryophytes, chlorophyta, and angiosperms. It can be useful for the study of homologous genes (that have maintained relative chromosomal positions) in sequenced genomes.
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.
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.
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.
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.
Supplies contents and method to study DNA sequences. Globin Gene Server informs about human hemoglobin mutations. It offers a list of experimental data and several types of software allowing comparison to find regions that are likely to play significant roles.
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.
A collaborative competition to assess the state of the art in whole genome sequence alignment. The Alignathon is a collaborative project to assess whole genome aligners and promote development of the field of whole genome alignment. Alignathon is inspired by the Assemblathon project, an iterative collaborative competition to assess the state of the art in de novo genome assembly.