IprScan predicts InterPro domains based on protein sequences [56]

IprScan predicts InterPro domains based on protein sequences [56]. The

Interpro2go mapping file (http://​www.​ebi.​ac.​uk/​interpro) was used to map GO annotations to genes with the corresponding domain predictions. A domain-based GO prediction was made only if it was not redundant with an existing manually-curated or orthology-based GO term, or one of its parental terms, that was already assigned to an orthologous protein. Finally, descriptions for genes lacking manual or GO-based annotations were constructed from the manual GO terms assigned to MDV3100 manufacturer characterized orthologs. GO annotations were included with the following precedence: BP, followed by MF, and then CC. For genes that lacked experimental characterization and characterized orthologs, but had functionally characterized InterPro domains, descriptions were generated from the domain-based GO annotations. The same precedence rules applied as to the descriptions selleck generated using orthology-based GO information. For genes that

lacked experimental characterization and characterized PR-171 datasheet orthologs, and without functionally characterized InterPro domains, but had uncharacterized orthologs, the descriptions simply list the orthology relationship because no inferred GO information was available. Secondary metabolic gene cluster analysis and annotation The pre-computed results file (smurf_output_precomputed_08.13.08.zip) was downloaded from the SMURF website (http://​jcvi.​org/​smurf/​index.​php). Version 1.2.1 of the antiSMASH program [39] was downloaded from (http://​antismash.​secondarymetabol​ites.​org/​) and run locally on the chromosome and/or contig sequences of A. nidulans FGSC A4, A. fumigatus Af293, A. niger CBS 513.88 and A. oryzae RIB40. Details of the parameters the antiSMASH program uses to predict boundaries are in described in Medema et al. 1998 [39] and those for SMURF are described in Khaldi et al. 2010 [38]. The secondary metabolic gene clusters predicted by

these programs P-type ATPase were manually analyzed and annotated using functional data available for each gene in AspGD. Cluster membership was determined based on physical proximity of candidate genes to cluster backbone genes. Adjacent genes were added to the cluster if they had functional annotations common to known secondary metabolism genes. In cases where backbone genes had Jaccard orthologs in other species (see above), we required orthology between all other cluster members. Confirmation of orthology between clusters was facilitated by use of the Sybil multiple genome browser which can be used to evaluate synteny between species. We visually evaluated synteny by examining whether a gene that was putatively in a cluster had orthologs in the other species – where a gene in the species in which the cluster was identified no longer had orthologs in the other species that were adjacent, we inferred a break in synteny.

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