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Pipeline publication

[…] (http://www.jgi.doe.gov/genome-projects), or at the NITE Institute database (http://www.bio.nite.go.jp/dogan)., Furthermore, we assessed the phylogenetic relationships between all putative ATP-binding cassette (ABC) transporters from F. graminearum. The identification of such proteins relied on the FunCat and GO annotations described above. FGDB provided 78 genes annotated in the FunCat category 'ABC transporters' (20.03.25). Manual revision appeared to be necessary since this list also contained MFS (= major facilitator superfamily) transporters and other non-ABC proteins. Beyond those, we excluded four additional proteins that lacked any transmembrane domains, which were identified by the TMHMM software (http://www.cbs.dtu.dk/services/TMHMM/), resulting in a set of 50 putative ABC transporters. In a second analysis using the GO annotations, we applied the GO term 'ATPase activity, coupled to transmembrane movement of substances' (GO:042626). This recovered four additional proteins that were not found by FunCat and which were included in the molecular phylogeny. To assign all identified ABC transporters to one of the known subfamilies [,] we analyzed the distribution of predicted transmembrane and ATP binding domains by the TMHMM (see above) and the Conserved Domain Search (CDS) softwares (http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml). In addition, BlastP searches using ABC transporters from S. cerevisiae and C. albicans as queries assisted in the classification of the corresponding F. graminearum proteins., Predicted putative F. graminearum transcription factors were obtained from the Fungal Transcription Factor Database (FTFD) (http://ftfd.snu.ac.kr/). Transcription factors whose transcript levels differed significantly between the control and the fungicide treatment in the microarray experiments were used as queries in BlastP searches against the proteomes of S. cerevisiae (at SGD; see above) and Candida albicans (CGD; http://www.candidagenome.org). Vice versa, best hits were used for BlastP searches against the F. graminearum proteome., For phylogenetic analyses, we used the software MEGA version 4 []. Alignments were created by the implemented ClustalW algorithm, using the substitution BLOSUM weight matrix and the following parameters. For pairwise and multiple alignment the gap opening penalty was set to 10, whereas the gap extension penalties were set to 0.1, and respectively 0.05. Evolutionary history was inferred using the Neighbor-Joining method. Evolutionary distances were computed using the Poisson correction method. Gaps and missing data were eliminated only from pairwise sequence comparisons (Pairwise deletion option). The confidence of the resulting tree was estimated with 1000 bootstrap iterations., Microarray data analyzing in F. graminearum two nutritional stress conditions, i.e. carbon and nitrogen starvation, were p […]

Pipeline specifications

Software tools TMHMM, BLASTP, MEGA, Clustal W
Databases FunCat
Organisms Fusarium graminearum, Triticum aestivum
Chemicals Azoles, Steroids