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Protocols

COGEME specifications

Information


Unique identifier OMICS_03101
Name COGEME
Restrictions to use None
Maintained No

Publication for COGEME

COGEME citations

 (11)
library_books

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

2015
BMC Genomics
PMCID: 4546252
PMID: 26296655
DOI: 10.1186/s12864-015-1836-2

[…] against the NCBInr protein database using the BLASTX algorithm (http://www.ncbi.nlm.nih.gov/BLAST) and against the Consortium for the Functional Genomics of Microbial Eukaryotes EST database (http://cogeme.ex.ac.uk) using TBLASTX algorithm []. An ORF finder algorithm (http://www.ncbi.nlm.nih.gov/gorf) was employed to predict coding regions of candidate effectors in all six frames ab initio; the l […]

library_books

The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

2015
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 […]

library_books

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

2015
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 (www.broad.mit.edu/annotation/genome/verticillium_dahliae/), FASTA-UK, among others. The predicted proteins based on the best ORFs (NCBI-ORF) were also determin […]

call_split

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

2015
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 (http://cogeme.ex.ac.uk) websites. Protein sequence alignments and phylogenetic trees were obtained using ClustalW and MEGA 5.1 []. […]

call_split

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

2014
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 […]

library_books

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

2014
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., ; www.phi-base.org); 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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