OrthoMCL-DB statistics

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OrthoMCL-DB specifications

Information


Unique identifier OMICS_05343
Name OrthoMCL-DB
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Subtool


  • OrthoMCL

Maintainers


  • person_outline David Roos
  • person_outline Steve Fischer
  • person_outline OrthoMCL-DB Team

Publications for OrthoMCL-DB

OrthoMCL-DB citations

 (12)
library_books

Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low Copy Nuclear Genes

2016
Genome Biol Evol
PMCID: 5631032
PMID: 27604879
DOI: 10.1093/gbe/evw196

[…] To identify marker genes for eukaryotic phylogeny, we screened OrthoMCL-DB () (version 4), which delineated putative groups of orthologous genes (orthogroups) from 88 eukaryotic and 50 prokaryotic genomes. The taxon sampling in OrthoMCL-DB was biased toward well- […]

library_books

Sugarcane Giant Borer Transcriptome Analysis and Identification of Genes Related to Digestion

2015
PLoS One
PMCID: 4338194
PMID: 25706301
DOI: 10.1371/journal.pone.0118231

[…] by annotation, sequence similarities and InterPro terms.Digestive enzyme sequences were submitted to the online tool TRAPID [] for comparative analysis of SGB transcripts and the B. mori genome. The OrthoMCL-DB proteome database was used as a reference. Protein family groups were identified and organized accordingly to the gene expansion or depletion information. […]

library_books

The Chironomus tentans genome sequence and the organization of the Balbiani ring genes

2014
BMC Genomics
PMCID: 4192438
PMID: 25261295
DOI: 10.1186/1471-2164-15-819

[…] nscripts (adding 206 gene loci) were added to the initial set. The final set of predicted genes thus contained 15,120 gene loci.All protein-coding genes were classified into protein families based on orthoMCL-DB v5 [] using the longest predicted protein sequence for each gene loci. A phylogenietic tree (Additional file : Figure S2) was reconstructed (RAxML v7.2.8, PROTGAMMAJTTF model, 100 bootstra […]

library_books

Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes

2014
BMC Genomics
PMCID: 3932018
PMID: 24417976
DOI: 10.1186/1471-2164-15-23

[…] ools.org.uk/pise/double_act.html# with a cutoff score of 0. Comparisons of regions flanking the PZ were performed using default blastn settings in EasyFig []. Orthologous gene sets were identified by OrthoMCL-DB using reciprocal blastp with a cutoff of e-5 and 50% match []. Genome maps were generated using the CGView Server []. […]

library_books

Variant surface antigens of malaria parasites: functional and evolutionary insights from comparative gene family classification and analysis

2013
BMC Genomics
PMCID: 3747859
PMID: 23805789
DOI: 10.1186/1471-2164-14-427

[…] si KIR protein PKH_114850; P. yoelii hypothetical protein PY06119; P. berghei BIR protein PBANKA_010050; and P. chabaudi CIR protein PCHAS_010120. Orthology of these five PIR proteins is supported by OrthoMCL DB (version 5.0, orthologous group OG5_173782) [] and by the fact that gene synteny is conserved among the five species (PlasmoDB 9.3). Multiple sequence alignment of the five conserved PIR o […]

library_books

Functional genomics of a generalist parasitic plant: Laser microdissection of host parasite interface reveals host specific patterns of parasite gene expression

2013
BMC Plant Biol
PMCID: 3636017
PMID: 23302495
DOI: 10.1186/1471-2229-13-9

[…] tensive efforts detailed above were translated based on the ESTScan ORF prediction and submitted to InterProScan [] via blast2go [] using default parameters. These unigenes were also submitted to the OrthoMCL DB [] database using default parameters.The unigenes with the greatest RPKM in unique and overlapping Orthogroups, excluding those belonging to Orthogroups shared in all three transcriptomes […]

Citations

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OrthoMCL-DB institution(s)
Center for Bioinformatics, University of Pennsylvania, Philadelphia PA, USA; Department of Biology, University of Pennsylvania, Philadelphia PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia PA, USA; Bayer Business and Technology Services, Bayer Healthcare Pharmaceuticals, NJ, USA
OrthoMCL-DB funding source(s)
Supported by the National Institute of Allergy and Infectious Diseases at the National Institutes of Health [Award NO1-AI900038C Contract No. HHSN272200900038C].

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