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COGEME specifications


Unique identifier OMICS_03101
Restrictions to use None
Maintained No

Publication for COGEME

COGEME citations


Candidate effectors contribute to race differentiation and virulence of the lentil anthracnose pathogen Colletotrichum lentis

BMC Genomics
PMCID: 4546252
PMID: 26296655
DOI: 10.1186/s12864-015-1836-2

[…] against the NCBInr protein database using the BLASTX algorithm ( and against the Consortium for the Functional Genomics of Microbial Eukaryotes EST database ( using TBLASTX algorithm []. An ORF finder algorithm ( was employed to predict coding regions of candidate effectors in all six frames ab initio; the l […]


The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

BMC Genomics
PMCID: 4511438
PMID: 26198851
DOI: 10.1186/s12864-015-1756-1

[…] US (version 2.7) [] using F. graminearum species model, GeneMark [] and SNAP [], which was trained using all the Fusarium proteins in UNIPROT with the keyword “Fusarium” which had evidence, ESTs from Cogeme [], and trinity assemblies using RNA-seq from the mycelium and spores of PH-1, and wild type Z-3639. This evidence was provided to MAKER as hints to the annotation. The final annotation set pro […]


A cupin domain containing protein with a quercetinase activity (VdQase) regulates Verticillium dahliae's pathogenicity and contributes to counteracting host defenses

Front Plant Sci
PMCID: 4462102
PMID: 26113857
DOI: 10.3389/fpls.2015.00440

[…] for any potential misinterpretation and submitted to a BLAST search for potential matches with stored sequences in the GeneBank. The cDNA sequences were also matched against other databases including Cogeme, MIT-Verticillium Genome project (, FASTA-UK, among others. The predicted proteins based on the best ORFs (NCBI-ORF) were also determin […]


Methionine Biosynthesis is Essential for Infection in the Rice Blast Fungus Magnaporthe oryzae

PLoS One
PMCID: 4391826
PMID: 25856162
DOI: 10.1371/journal.pone.0111108
call_split See protocol

[…] zae genome sequence version 8 and the corresponding CDS and gene nomenclature (v7) available at the Broad Institute, were used in this study. M. oryzae ESTs were searched using BlastN at the NCBI and COGEME ( websites. Protein sequence alignments and phylogenetic trees were obtained using ClustalW and MEGA 5.1 []. […]


Gene expression profiling of candidate virulence factors in the laminated root rot pathogen Phellinus sulphurascens

BMC Genomics
PMCID: 4117978
PMID: 25030912
DOI: 10.1186/1471-2164-15-603
call_split See protocol

[…] category following the Munich Information Center for Protein Sequences Functional Categories (MIPS FunCat) annotation scheme []. The assignment of ESTs to these categories was aided in large part by COGEME []: a tBLASTx search (translated nucleotide database search using translated nucleotide query) of the COGEME database with the Ps sequences produced ranked matches as well as their functional c […]


Overview of the functional virulent genome of the coffee leaf rust pathogen Hemileia vastatrix with an emphasis on early stages of infection

Front Plant Sci
PMCID: 3953675
PMID: 24672531
DOI: 10.3389/fpls.2014.00088

[…] logous Group (KOG) database (Tatusov, ); the Pathogen-Host Interaction (PHI-base v3.2) reference database (Winnenburg et al., ;; the Phytopathogenic Fungi and Oomycete EST Database (COGEME v1.6; Soanes and Talbot, ); and a Pucciniales EST database (168,199 ESTs retrieved from GenBank in November 2012—unchanged number as of December 2013). Besides these, 16,831 transcripts from th […]


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COGEME institution(s)
School of Biosciences, University of Exeter, Washington Singer Laboratories, Exeter, UK

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