Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies.
Integrates data sets from a range of experiments and model organisms alongside tools for exploring them. The current version brings together information covering genes, proteins, orthologues, interactions, gene expression, pathways, ontologies, diseases, genome-wide association studies and single nucleotide polymorphisms. Although the emphasis is on human data, key data sets from mouse and rat are included.
Helps biologists to find the flanking insertion sites (FSTs) that interrupt the genes in which they are interested. The FLAGdb information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge.
A database for Brassica crops at the whole genome scale. BRAD provides several datasets, like the complete Brassica A genome sequence from Brassica rapa (B. rapa), coming from de novo assembly of sequence scaffolds. Also included are predicted genes and associated annotations (with diverse link to other DB, like InterPro, KEGG2, SwissProt), and B. rapa genes orthologous to those in Arabidopsis thaliana, as well as genetic markers and maps of B. rapa.
Provides data about the model organism Paramecium tetraurelia. ParameciumDB was created by using components of the Generic Model Organism Database (GMOD). It offers data about gene expression data from genome-wide transcriptome experiments using a NimbleGen custom microarray platform. The database can be consulted through a detailed view that provides protein alignments and links to external databases.
Provides sets of gene predictions and orthologous groups for six clades. OPTIC is designed to provide pre-calculated phylogenetic datasets that are benefit to clade genomic analyses. A useful feature of the database is its provision of multiple alignments either for genes as concatenated exons, or for alternative transcripts. For each orthologous group, OPTIC indicates transcript predictions, orthologs, multiple alignments and phylogenetic trees.
Provides orthology information about originally annotated human genes in the H-Invitational database (H-InvDB). Evola contains two datasets (i) a comprehensive set of orthologs and (ii) more reliable orthologs supported by manual curation. Besides orthology information can be used with close reference to other annotation in H-InvDB. The database includes over 18 968 human genes among 11 vertebrates as well as chimpanzee, macaque, cow, or Fugu.