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Found 7 result(s)

Ensembl Metazoa

e!EnsemblMetazoa

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Ensembl Metazoa is a genome-centric portal for metazoan species of scientific interest.

eLibrary of Microbial Systematics and Genomics

eLMSG

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eLMSG (eLibrary of Microbial Systematics and Genomics) is a web microbial library that integrates not only taxonomic information, but also genomic information and phenotypic information (including morphology, physiology, biochemistry and enzymology). The taxonomic system of eLMSG is manually curated and composed of all validly and some effectively published taxa. For each taxon, the Latin name, taxon ID (NCBI taxonomy), etymology, rank, lineage, the dates of effective and/or valid publication, feature descriptions, nomenclature type and references for the proposal and emendations during the history of the taxon are presented. Besides these data, the species taxa contain information about 16S rRNA gene and/or genome sequences. All publicly available genome data of each type species including both type and non-type strains were collected, and if needed, re-annotated using the standardized analysis pipeline. Furthermore, pan-genomic data analyses were conducted for species with ≥5 genome sequences available. Finally, for all type species, taxonomically relevant phenotypic data were extracted and curated from literatures, which were further indexed into eLMSG as searchable and analyzable data records. Taken together, eLMSG is a comprehensive web platform for studying mi- crobial systematics and genomics, potentially useful for better understanding microbial taxonomy, natural evolutionary processes and ecological relationships.

Ensembl Protists

e!EnsemblProtists

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EnsemblProtists is a genome-centric portal for protists species.

Ensembl Bacteria

e!EnsemblBacteria

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This site provides access to complete, annotated genomes from bacteria and archaea (present in the European Nucleotide Archive) through the Ensembl graphical user interface (genome browser). Ensembl Bacteria contains genomes from annotated INSDC records that are loaded into Ensembl multi-species databases, using the INSDC annotation import pipeline.

NCBI Gene

Gene

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The Gene database provides detailed information for known and predicted genes defined by nucleotide sequence or map position. Gene supplies gene-specific connections in the nexus of map, sequence, expression, structure, function, citation, and homology data. Unique identifiers are assigned to genes with defining sequences, genes with known map positions, and genes inferred from phenotypic information. These gene identifiers are used throughout NCBI's databases and tracked through updates of annotation. Gene includes genomes represented by NCBI Reference Sequences (or RefSeqs) and is integrated for indexing and query and retrieval from NCBI's Entrez and E-Utilities systems.

GOBASE

The Organelle Genome Database

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!!! >>> the repository is offline >>> !!! GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts. GOBASE is currently expanding to include information on representative bacteria that are thought to be specifically related to the bacterial ancestors of mitochondria and chloroplasts

The Adaptive Evolution Database

TAED

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TAED is a database of phylogenetically indexed gene families. It contains multiple sequence alignments from MAFFT1, maximum likelihood phylogenetic trees from PhyML2, bootstrap values for each node, dN/dS ratios for each lineage from the free ratios model in PAML3, and labels for each node of speciation or duplication from gene tree/species tree reconciliation using SoftParsMap4. The phylogenetic indexing enables simultaneous viewing of lineages with high dN/dS that occurred along the same species tree branches. Resources from the Protein Data Bank (PDB) and the Kyoto Encyclopedia of Genes and Genomes (KEGG)5, have been incorporated into the TAED analysis to detect substitutions along each branch within the phylogenetic tree and to assess selection within pathways.