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Protocols

OrthoDB specifications

Information


Unique identifier OMICS_01692
Name OrthoDB
Restrictions to use None
Community driven No
Data access File download, Browse, Application programming interface
User data submission Not allowed
Version 10
Content license CC Attribution
Maintained Yes

Documentation


Maintainer


  • person_outline Evgeny M. Zdobnov

Additional information


https://www.orthodb.org/?page=help

Publications for OrthoDB

OrthoDB citations

 (142)
library_books

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes

2018
BMC Genomics
PMCID: 5954271
PMID: 29764366
DOI: 10.1186/s12864-018-4466-7

[…] We retrieved homologous gene families from orthologous gene groups of 21 Culicidae species recovered from the OrthoDBmoz2 database (http://cegg.unige.ch/orthodbmoz2) generated using OrthoDB []. We generated a multiple sequence alignment for each family, used RAXML [] to compute draft gene trees with bootstrap supports, and then corrected these draft gene trees using PROFILENJ []. […]

library_books

Genome sequencing of Rhinorhipus Lawrence exposes an early branch of the Coleoptera

2018
Front Zool
PMCID: 5930637
PMID: 29743928
DOI: 10.1186/s12983-018-0262-0

[…] them for irregularities. Removal of low-quality reads and TruSeq adaptor sequences (Illumina Inc., San Diego, CA) was performed with Trimmomatic-0.36 [].The ortholog set was obtained by searching the OrthoDB 9.1 database [] for one-to-one orthologs among Coleoptera in available genome sequences of Agrilus planipennis, Anoplophora glabripennis, Dendroctonus ponderosae, Leptinotarsa decemlineata, On […]

library_books

De Novo DNA Synthesis in Aedes aegypti Midgut Cells as a Complementary Strategy to Limit Dengue Viral Replication

2018
Front Microbiol
PMCID: 5932203
PMID: 29755433
DOI: 10.3389/fmicb.2018.00801

[…] otide sequences from Drosophila melanogaster database2 (Gramates et al., ) were used as bait, screening the afore mentioned databases using BLAST program (default parameters).To localize orthologues, OrthoDB online program was used (Zdobnov et al., ), and for protein properties (family, domains and repeats, gene ontology term prediction and protein architecture) InterproScan website was used (Finn […]

library_books

A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

2018
BMC Genomics
PMCID: 5896114
PMID: 29642853
DOI: 10.1186/s12864-018-4647-4

[…] genes identified by Ensembl Compara, we also used HomoloGene (https://www.ncbi.nlm.nih.gov/homologene) [], TreeFam (Release 9, March 2013, 109 species, 15,736 families) (http://www.treefam.org/) and OrthoDB v9 (http://www.orthodb.org/) and assessed orthology based on RBH (reciprocally best hit, performing an NCBI BLASTP search using the default parameters). We also manually verified each genome-s […]

library_books

Signatures of DNA Methylation across Insects Suggest Reduced DNA Methylation Levels in Holometabola

2018
Genome Biol Evol
PMCID: 5915941
PMID: 29697817
DOI: 10.1093/gbe/evy066

[…] ofile Hidden Markov Models (pHMMs) for the proteins in question (all pHMMs are available at: doi: 10.17632/8y5wm8887b.3). Amino-acid sequences of arthropod DNMTs and Tet proteins were downloaded from OrthoDB using the text-based search option (; ). Subsequently, we aligned each group of orthologous sequences using MAFFT L-INSI () and generated pHMMs from each alignment using HMMER 3.1b1 (www.hmmer […]

library_books

A draft genome sequence for the Ixodes scapularis cell line, ISE6

2018
F1000Res
PMCID: 5883391
PMID: 29707202
DOI: 10.5256/f1000research.14813.r31696

[…] sion 2.2.6 for several values of K: 11, 15, 21, 41, 51, and 61. Each computed K-mer histogram was analyzed with GenomeScope ( ). Single-copy gene analysis used BUSCO ( ) version 3.0.2 with Arthropoda OrthoDB version 9. Alignments between the tick and cell line assemblies were computed on contigs from each assembly using nucmer, the local aligner in the MUMmer package ( ) version 3.1. The BLAST ana […]


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OrthoDB institution(s)
Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; Swiss Institute of Bioinformatics, Geneva, Switzerland
OrthoDB funding source(s)
Supported byUniversity of Geneva and Swiss National Science Foundation Grant [31003A 166483]; Swiss Institute of bioinformatics SERI; University of Geneva COINF; Sao Paulo Research Foundation [17/15195-2].

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