Computational protocol: Comparative analysis of the repertoire of G protein-coupled receptors of three species of the fungal genus Trichoderma

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Protocol publication

[…] Version 2 of the T. atroviride genome database [] comprises 11,863 gene models on 29 scaffolds; version 2 of the T. virens genomic sequence [] comprises 12,427 gene models on 93 scaffolds. For the homology-based search of GPCR-like proteins from T. atroviride and T. virens, the genomic sequences and deduced proteomes of the following fungi were used: Trichoderma reesei[]Aspergillus nidulans, Aspergillus fumigatus, Aspergillus oryzae[], Neurospora crassa[], Magnaporthe grisea[], Podospora anserine[], Chaetomium globosum[], Fusarium graminearum[], and Nectria haematococca[]. An e-value limit of 1e-09 was applied.To identify putative GPCRs within the T. atroviride and T. virens proteomes that lack significant sequence similarity to known GPCR-like proteins and therefore may escape detection by homology search, a more sensitive database searching using hidden Markov models (HMM) was performed using the program HMMER (http://hmmer.janelia.org/) [].All obtained predicted proteins were analyzed with the TMHMM, ConPred II and HMMTOP algorithms [-] to test for the typical 7-transmembrane domain topology. For those few proteins exhibiting less than seven transmembrane domains, the respective encoding gene and flanking regions were retrieved from the genome database and examined manually. Wrongly predicted intron-exon boundaries were mainly found and manually corrected resulting in the detection of the missing transmembrane domains. […]

Pipeline specifications

Software tools HMMER, TMHMM, ConPred, HMMTOP
Application Membrane protein analysis
Organisms Trichoderma virens, Trichoderma reesei, Trichoderma atroviride
Diseases Mycoses