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Comparative genome databases | Comparative genomics

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…
EuMicrobedbLite
Dataset

EuMicrobedbLite

A light weight comprehensive genome resource and sequence analysis platform for…

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…

Pseudomonas…
Dataset

Pseudomonas Genome Database

Collaborates with an international panel of expert Pseudomonas researchers to…

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…

CyanoBase
Dataset

CyanoBase

Provides an easy way of accessing the sequences and all-inclusive annotation…

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…

Gramene
Dataset

Gramene

Offers comparative functional genomics in crops and model plant species.…

Offers comparative functional genomics in crops and model plant species. Gramene uses information generated from projects supported by public funds in order to facilitate the study of cross-species…

PGSB PlantsDB
Dataset

PGSB PlantsDB Plant Genome and Systems Biology PlantsDB

A database framework for the comparative analysis and visualization of plant…

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…

Triticum Urartu
Dataset

Triticum Urartu

A database which offers gene annotation of triticum urartu is the diploid…

A database which offers gene annotation of triticum urartu is the diploid progenitor of the bread wheat A-genome. Also known as red wild einkorn, is a diploid species whose genome is the A genome of…

Anolis…
Dataset

Anolis carolinensis

A database which offers gene annotation of Anolis carolinensis also known as…

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…

Tetraodon…
Dataset

Tetraodon nigroviridis

A database which offers gene annotation of Tetraodon nigroviridis also known as…

A database which offers gene annotation of Tetraodon nigroviridis also known as green spotted puffer. The Tetraodon genome was sequenced using the whole-genome shotgun (WGS) approach. The Tetraodon…

Aegilops…
Dataset

Aegilops tauschii

A database which offers assembly and gene annotation of Aegilops tauschii, also…

A database which offers assembly and gene annotation of Aegilops tauschii, also known as Tausch's goatgrass. The diploid progenitor of the bread wheat D-genome provides important evolutionary…

Phytozome
Dataset

Phytozome

Provides a centralized hub for plant genome and gene family data and analysis.…

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…

GeneOrder
Web

GeneOrder

Compares gene order between two small genomes. Gene Order is a web-based…

Compares gene order between two small genomes. Gene Order is a web-based interactive computational tool which determines the collinearity of genes between two genomes. The software has been tested on…

YGOB
Dataset

YGOB Yeast Gene Order Browser

Facilitate visual comparisons and computational analysis of synteny…

Facilitate visual comparisons and computational analysis of synteny relationships in yeasts.

Ensembl Genomes
Dataset

Ensembl Genomes

An integrating resource for genome-scale data from non-vertebrate species.

An integrating resource for genome-scale data from non-vertebrate species.

Anopheles…
Dataset

Anopheles gambiae

A database offering the genome sequence of Anopheles gambiae, the primary…

A database offering the genome sequence of Anopheles gambiae, the primary mosquito vector responsible for the transmission of malaria in most of sub-Saharan Africa. It is a member of a species…

Xenbase
Dataset

Xenbase

Integrates variety of data from biomedical model genus and archives large data…

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…

PGDD
Dataset

PGDD Plant Genome Duplication Database

A public database to identify and catalog plant genes in terms of intragenome…

A public database to identify and catalog plant genes in terms of intragenome or cross-genome syntenic relationships.

GreenPhylDB
Dataset

GreenPhylDB

A web resource designed for comparative and functional genomics in plants.…

A web resource designed for comparative and functional genomics in plants. GreenPhylDB contains a catalogue of gene families based on gene predictions of genomes, covering a broad taxonomy of green…

MolliGen
Dataset

MolliGen

A database dedicated to the comparative genomics of bacteria belonging to the…

A database dedicated to the comparative genomics of bacteria belonging to the class Mollicutes.

CGUG
Web

CGUG CoreGenesUniqueGenes

Performs iterative BLASTP analyses employing a reference genome and up to four…

Performs iterative BLASTP analyses employing a reference genome and up to four query genomes to provide a table of genes common to these genomes. The CGUG web app can be used for re-annotating small…

CoreGenes
Web

CoreGenes

Determines the core set of genes in a group of small genomes. CoreGenes is a…

Determines the core set of genes in a group of small genomes. CoreGenes is a global JAVA-based interactive data mining tool which allows for the identification, characterization, catalog and…

LegumeIP
Dataset

LegumeIP

Hosts large-scale genomics and transcriptomics data and provides integrative…

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…

ATGC
Dataset

ATGC Alignable Tight Genomic Clusters

A database of closely related microbial genomes optimized for microevolutionary…

A database of closely related microbial genomes optimized for microevolutionary research.

Nematode.net
Dataset

Nematode.net

Disseminates diverse bioinformatic data sets and provide analysis tools to the…

Disseminates diverse bioinformatic data sets and provide analysis tools to the broad scientific community in a useful and user-friendly manner. Next-generation data has been added to the various…

Comparasite
Dataset

Comparasite

A database for comparative studies of transcriptomes of parasites.

A database for comparative studies of transcriptomes of parasites.

TAED
Dataset

TAED The Adaptive Evolution Database

Provides a resource for bioinformaticists interested in data mining and for…

Provides a resource for bioinformaticists interested in data mining and for experimental evolutionists seeking candidate examples of adaptive evolution for further experimental study.

CFGP
Dataset

CFGP Comparative Fungal Genomics Platform

Archives 283 genomes corresponding to 152 fungal and Oomycete species as well…

Archives 283 genomes corresponding to 152 fungal and Oomycete species as well as 201 genomes that correspond to seven bacteria, 39 plants and 105 animals.

ProPortal
Dataset

ProPortal

A database containing genomic, metagenomic, transcriptomic and field data for…

A database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus.

GabiPD
Dataset

GabiPD GABI Primary Database

Constitutes a repository and analysis platform for a wide array of…

Constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species.

CG
Dataset

CG Comparative Genometrics

Devoted to the characterization of complete chromosome sequences by…

Devoted to the characterization of complete chromosome sequences by standardized genometric methods.

ShiBASE
Dataset

ShiBASE

It focuses on the comparative genomics of Shigella and provides a way to…

It focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format.

Popset
Dataset

Popset

A collection of related sequences and alignments derived from population,…

A collection of related sequences and alignments derived from population, phylogenetic, mutation and ecosystem studies that have been submitted to GenBank. The population could originate from…

HGTree
Dataset

HGTree

Provides genome-wide horizontal gene transfer information for 2472 completely…

Provides genome-wide horizontal gene transfer information for 2472 completely sequenced prokaryotic genomes (156 Archaea and 2316 Bacteria). HGTree defines lateral gene transfer by comparing the gene…

PlanMine
Dataset

PlanMine

Aims to provide an easily accessible and minable repository of general…

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…

InsectBase
Dataset

InsectBase

Provides a comprehensive platform for researchers who have interests in…

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,…

MBGD
Dataset

MBGD Microbial genome database for comparative analysis

A comprehensive ortholog database for flexible comparative analysis of…

A comprehensive ortholog database for flexible comparative analysis of microbial genomes, where the users are allowed to create an ortholog table among any specified set of organisms. The MyMBGD…

DBETH
Dataset

DBETH Database for Bacterial ExoToxins

The main objective of this database is to provide a comprehensive knowledgebase…

The main objective of this database is to provide a comprehensive knowledgebase for human pathogenic bacterial toxins where various important sequence, structure and physico-chemical property based…

LEGER
Dataset

LEGER

Supports functional Listeria genome analyses by combining information obtained…

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…

EDGAR
Web

EDGAR

Serves to search and retrieve data from microbial genomes and to compare…

Serves to search and retrieve data from microbial genomes and to compare genomics sequences. EDGAR procures extended phylogenetic analysis features as AAI (Average Amino Acid Identity) or ANI…

CiF
Dataset

CiF Cyber infrastructure for Fusarium

Supports archiving and utilization of rapidly increasing data and knowledge and…

Supports archiving and utilization of rapidly increasing data and knowledge and consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The…

BrucellaBase
Dataset

BrucellaBase

A web-based platform that provides features of a genome database together with…

A web-based platform that provides features of a genome database together with unique analysis tools. We have developed a web version of the multilocus sequence typing (MLST) and phylogenetic…

MOsDB
Dataset

MOsDB MIPS Rice (Oryza sativa) DataBase

A resource for publicly available sequences of the rice (Oryza sativa L.)…

A resource for publicly available sequences of the rice (Oryza sativa L.) genome. MOsDB provides all available data about rice genes and genomics, including (in the future) mutant information and…

VigGS
Dataset

VigGS Vigna Genome Server

A genome database of the genus Vigna based on the recently sequenced azuki bean…

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,…

MetaMicrobesOnl…
Dataset

MetaMicrobesOnline

Offers phylogenetic analysis of genes from microbial genomes and metagenomes.

Offers phylogenetic analysis of genes from microbial genomes and metagenomes.

Coffee Genome…
Dataset

Coffee Genome Hub

An integrative genome information system that allows centralized access to…

An integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee. The hub relies on…

Trematode.net
Dataset

Trematode.net

A site dedicated to the dissemination of data from flukes, flatworm parasites…

A site dedicated to the dissemination of data from flukes, flatworm parasites of the class Trematoda, phylum Platyhelminthes. Trematode.net is an independent component of Helminth.net and currently…

Helminth.net
Dataset

Helminth.net

A collection of worm-related databases and analysis tools. Currently the sites…

A collection of worm-related databases and analysis tools. Currently the sites Nematode.net and Trematode.net fall under the Helminth.net umbrella. The databases' interface, with a sophisticated…

MyMpn
Dataset

MyMpn

An online resource devoted to studying the human pathogen Mycoplasma…

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…

BGD
Dataset

BGD Bat Genome Database

An open-access, web-available portal that integrates available data of bat…

An open-access, web-available portal that integrates available data of bat genomes and genes. BGD hosts data from six bat species, including two megabats and four microbats. Users can query the gene…

SPODOBASE
Dataset

SPODOBASE

An integrated database for the genomics of the Lepidoptera Spodoptera…

An integrated database for the genomics of the Lepidoptera Spodoptera frugiperda.

pico-PLAZA
Dataset

pico-PLAZA

A web-based resource for algal genomics that combines different data types with…

A web-based resource for algal genomics that combines different data types with intuitive tools to explore genomic diversity, perform integrative evolutionary sequence analysis and study gene…

Pristionchus.or…
Dataset

Pristionchus.org

Offers diverse content covering genome browsing, genetic and physical maps,…

Offers diverse content covering genome browsing, genetic and physical maps, similarity searches, a community platform and assembly details. Content will be continuously improved and will be an…

CottonGen
Dataset

CottonGen

A curated and integrated web-based relational database providing access to…

A curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker…

GDR
Dataset

GDR Genome Database for Rosaceae

A central repository of curated and integrated genetics and genomics data of…

A central repository of curated and integrated genetics and genomics data of Rosaceae, an economically important family which includes apple, cherry, peach, pear, raspberry, rose and strawberry.

OryGenesDB
Dataset

OryGenesDB

A search database for rice reverse genetics. OryGenesDB contains flanking…

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…

BmuG@Sbase
Dataset

BmuG@Sbase

Contains microbial gene expression and comparative genomic hybridization…

Contains microbial gene expression and comparative genomic hybridization experimental data. BµG@Sbase is a web-browsable Minimum Information about a Microarray Experiment (MIAME)-compliant database…

MuGI
Desktop

MuGI Multiple Genome Index

A compressed index of collections of genomes of the same species. MuGI reports…

A compressed index of collections of genomes of the same species. MuGI reports all occurrences of a given pattern, in exact and approximate matching model, against a collection of thousand(s)…

Oar
Dataset

Oar Ovis aries reference

Represents a gene expression atlas dataset. The O. aries reference genome (Oar…

Represents a gene expression atlas dataset. The O. aries reference genome (Oar v3.1) includes 27,504 loci that are transcribed (20,921 protein coding), of which 25,350 (19,921 protein coding) (97%)…

BorreliaBase
Dataset

BorreliaBase

An online database for comparative browsing of borrelia genomes. BorreliaBase…

An online database for comparative browsing of borrelia genomes. BorreliaBase is currently populated with sequences from 35 genomes of eight lyme-borreliosis group borrelia species and 7…

Ciona savignyi
Dataset

Ciona savignyi

Offers gene annotation of Ciona savignyi also known as Pacific transparent sea…

Offers gene annotation of Ciona savignyi also known as Pacific transparent sea squirt. The assembly consists of 374 Reftigs, totalling 174 Megabases, with a Contig N50 of 141Kb and Reftig N50 size of…

Macropus…
Dataset

Macropus eugenii

Offers gene annotation of Macropus eugenii also known as tammar wallaby. The…

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…

NeisseriaBase
Dataset

NeisseriaBase

An online genome and annotation database for Neisseria, a genus consisting a…

An online genome and annotation database for Neisseria, a genus consisting a large group of Gram-negative aerobic commensal of mucosal surface in the human body. Currently NeisseriaBase comprises of…

Sinbase
Dataset

Sinbase

A web-based database with comprehensive sesame (Sesamum indicum L.) genomic,…

A web-based database with comprehensive sesame (Sesamum indicum L.) genomic, genetic and comparative genomic information. Sinbase includes sequences of assembled sesame pseudomolecular chromosomes,…

Bolbase
Dataset

Bolbase

A database for the Brassica oleracea genome data and comparative genomics…

A database for the Brassica oleracea genome data and comparative genomics information. The whole genome of B. oleracea is available, including nine fully assembled chromosomes and 1,848 scaffolds,…

TIGR Maize…
Dataset

TIGR Maize Database

A repository of publicly available maize genomic sequences.

A repository of publicly available maize genomic sequences.

CKB
Dataset

CKB Cyanobacterial KnowledgeBase

A free access database that contains the genomic and proteomic information of…

A free access database that contains the genomic and proteomic information of 74 fully sequenced cyanobacterial genomes belonging to seven orders. CKB also contains tools for sequence analysis. The…

reefgenomics
Dataset

reefgenomics

Aims to centralize genomic and transcriptomic data from marine organisms.…

Aims to centralize genomic and transcriptomic data from marine organisms. Besides providing convenient means to download sequences, reefgenomics provides a genome browser to explore available genomic…

Lepbase
Dataset

Lepbase

A genomic resource for the Lepidoptera, supporting a research community using…

A genomic resource for the Lepidoptera, supporting a research community using genomic approaches to understand evolution, speciation, olfaction, behaviour and pesticide resistance in a wide range of…

ArthropodaCyc
Dataset

ArthropodaCyc

A collection of databases dedicated to the arthropod metabolism reconstruction.…

A collection of databases dedicated to the arthropod metabolism reconstruction. ArthropodaCyc allows researchers to perform reliable metabolism comparisons of fully sequenced arthropods genomes.…

CRRD
Dataset

CRRD Chinchilla Research Resource Database

Provides investigators with easy access to relevant datasets and software tools…

Provides investigators with easy access to relevant datasets and software tools to enhance their research. The Chinchilla Research Resource Database contains a complete catalog of genes for…

PromBase
Dataset

PromBase

Contains various genomics sequence for 913 microbial genomes and structural…

Contains various genomics sequence for 913 microbial genomes and structural features. PromBase can serve as a valuable resource for comparative genomics study and help the experimentalist to rapidly…

PGDBj
Dataset

PGDBj Plant Genome DataBase Japan

Aims to integrate plant genome-related information from databases (DBs) and the…

Aims to integrate plant genome-related information from databases (DBs) and the literature. The PGDBj is comprised of three component DBs and a cross-search engine, which provides a seamless search…

Cyanidioschyzon…
Dataset

Cyanidioschyzon merolae

A database offering the genome sequence of the ultrasmall unicellular red alga…

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…

MycoCAP
Dataset

MycoCAP Mycobacterium Comparative Analysis Platform

A comparative analysis platform dedicated to the important genus Mycobacterium.…

A comparative analysis platform dedicated to the important genus Mycobacterium. MycoCAP currently provides information of 2108 genome sequences of at least 55 Mycobacterium spp. A number of intuitive…

RAP-DB
Dataset

RAP-DB Rice Annotation Project Database

A comprehensive set of gene annotations for the genome sequence of rice, Oryza…

A comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare.

CarrotDB
Web

CarrotDB

A Web-based genomic and transcriptomic database for D. carota. It offers the…

A Web-based genomic and transcriptomic database for D. carota. It offers the tools of Genome Map and Basic Local Alignment Search Tool.

HelmCoP
Dataset

HelmCoP Helminth Control and Prevention

An online resource built by integrating functional, structural and comparative…

An online resource built by integrating functional, structural and comparative genomic data from plant, animal and human helminthes, to enable researchers to develop strategies for drug, vaccine and…

MabsBase
Dataset

MabsBase

A user-friendly database providing access to whole-genome sequences of newly…

A user-friendly database providing access to whole-genome sequences of newly discovered M. abscessus strains as well as resources for whole-genome annotations and computational predictions.

HOMD
Web

HOMD Human Oral Microbiome Database

A body site-specific public database providing the scientific community with…

A body site-specific public database providing the scientific community with comprehensive information on prokaryote species that are present in the human oral cavity. This dynamic database provides…

Bgi-Ris
Dataset

Bgi-Ris

An integrated information resource and comparative analysis workbench for rice…

An integrated information resource and comparative analysis workbench for rice genomes.

CnidBase
Dataset

CnidBase Cnidarian evolutionary genomics dataBase

A tool for investigating the evolutionary, developmental and ecological factors…

A tool for investigating the evolutionary, developmental and ecological factors that affect gene expression and gene function in cnidarians.

STPD
Dataset

STPD Salinity Tolerant Poplar Database

An integrative database for salt-tolerant poplar genome biology. Currently the…

An integrative database for salt-tolerant poplar genome biology. Currently the STPD contains Populus euphratica genome and its related genetic resources. P. euphratica, with a preference of the salty…

ListeriaBase
Dataset

ListeriaBase

Facilitates comparative analysis of Listeria spp. ListeriaBase currently houses…

Facilitates comparative analysis of Listeria spp. ListeriaBase currently houses 850,402 protein-coding genes, 18,113 RNAs and 15,576 tRNAs from 285 genome sequences of different Listeria strains. It…

JESAM
Web

JESAM

Compares database sequence. JESAM alignment algorithm therefore uses dynamic…

Compares database sequence. JESAM alignment algorithm therefore uses dynamic programming only for the final alignments relying on the gross overall overlap being easy to find because the goal was…

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