Tag: comparative genomics

Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.

The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.

Environment for comparative genome analysis.

Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as s ...

The Integrated Microbial Genomes (IMG/M) aims to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE's Joint Genome Institute (JGI). It also serves as a community resource for analysis and an ...

The OMA (“Orthologous MAtrix”) project is a method and database for the inference of orthologs among complete genomes. The distinctive features of OMA are its broad scope and size, high quality of inferences, feature-rich web interface, availability ...

Since 2016, the IMG/VR database has provided access to the largest collection of viral sequences obtained from (meta)genomes. Here we present the 3rd version of IMG/VR, composed of 18,373 cultivated and 2,314,329 uncultivated viral genomes (UViGs), n ...

The Aspergillus Genome Database is a resource for genomic sequence data as well as gene and protein information for Aspergilli. This publicly available repository is a central point of access to genome, transcriptome and polymorphism data for the fun ...

The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) strives to collect all publicly available trait mapping data, i.e. QTL (phenotype/expression, eQTL), candidate gene and association data (GWAS), and copy number variations (CNV) mapped ...

Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.

Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). Bgee is based exclusively on curated "normal", healthy, expr ...

The Banana Genome Hub centralises databases of genetic and genomic data for the Musa acuminata crop, and is the official portal for the Musa genome resources.

HOGENOM is a phylogenomic database providing families of homologous genes and associated phylogenetic trees (and sequence alignments) for a wide set sequenced organisms.

A major part of this information gets extracted by manual annotation from the yeast literature, and results of the systematic functional analysis projects as well as cross-references to other in-house or external databases (NCBI, PIR, PEDANT, EMBL) p ...

The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the ST ...

The platform enables biologists to examine a gene, protein, compound or disease of interest in a global, biological, or clinical context.

The Comprehensive Microbial Resource (CMR) gives access to a central repository of the sequence and annotation of all complete public prokaryotic genomes as well as comparative genomics tools across all of the genomes in the database.

Nematode.net is the home page of the parasitic nematode EST project at The Genome Institute at Washington University in St. Louis. The site was established in 2000 as a component of the NIH-NIAID grant "A Genomic Approach to Parasites from the Phylum ...

The Effective database contains pre-calculated predictions of bacterial secreted proteins and of functional secretion systems. Effective bundles various tools to recognize Type III secretion signals, conserved binding sites of Type III chaperones, eu ...

GermOnline is a cross-species database gateway focusing on high-throughput expression data relevant for germline development, the meiotic cell cycle and mitosis in healthy versus malignant cells. The portal provides access to the Saccharomyces Genomi ...

HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.

GenoList is an integrated environment for comparative exploration of microbial genomes. The current release integrates genome data for over 700 species (Genome Reviews). The query and navigation user interface includes specialized tools for subtracti ...

ChlamDB is a comparative genomics database covering the entire Chlamydiae phylum as well as their closest relatives belonging to the Planctomycetes-Verrucomicrobiae-Chlamydiae (PVC) superphylum. Genomes can be compared, analyzed and retrieved using a ...

Genomic data on mollicutes

Prediction of intact secretion systems III, IV and VI in bacterial genomes by using a Support Vector Machine (SVM) approach.

Ortholog groups and trees for 66 proteomes inferred by Hieranoid 2

AncientMetagenomeDir is a community curated resource of metadata of all published shotgun-sequenced ancient metagenome or microbial genome-level enriched samples

The Spirochetes Genome Browser

CEGA, (Conserved Elements from Genomic Alignments), is a database of conserved vertebrate elements. This database provides acces to precomputed sets of conserved sequences from different species and at different levels of the vertebrate phylogeny.

Devoted to the characterization of complete chromosome sequences by standardized genometric methods, this website displays for sequenced genomes, three different genometric analyses: the DNA walk and the GC and TA skews during the initial phase. Alth ...

Intuitive and modular software platform designed to unify miRBase and independent miRNA data resources. It enables miRNA researchers to computationally address complex questions involving the multitude of miRNA data resources.

Genomicus-fungi is a genome browser that enables users to navigate in fungi genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Genomicus-protists is a genome browser that enables users to navigate in protists genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Genomicus-metazoa is a genome browser that enables users to navigate in metazoa genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Genomicus-tunicates is a genome browser that enables users to navigate in tunicates genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. It uses ANISEED (htt ...

The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cassava, Cacao, Coffee, Grass, Rice and Sugarcane, genome hubs provide ...

Genomicus-Plants is a genome browser that enables users to navigate in plants genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.