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Pipeline publication

[…] teins [] (BLASTX), and sugarcane EST database [] (BLASTN), at an e-value ≤1e-5. Gene names were assigned to the highest scored hit., The data was compared against the sugarcane chloroplast genome (GenBank: KU214867), sorghum mitochondrial genome (GenBank: NC_008360.1) and maize mitochondrial genome (GenBank: NC_007982), to detect the chloroplast and mitochondrial genes captured in assemblies. The transcription factor (TF)-encoding transcripts were annotated by comparing against the plant transcription factor database (PlantTFDB v3.0) [] and sugarcane transcription factor database (9,672 TFs from 48 TF families) []., Further transcript functions were annotated by RunIproScan v1.1.0 [], using InterProScan-5.19-58.0 [], mapping against the known protein domain database, ORF ≥30 aa. GO terms were enriched and plotted by WEGO []. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway mapping was done on the KEGG Automatic Annotation Server (KAAS) v2.0 [], taking all plant species as references, GHOSTX and bi-directional best hit method., Transcripts were aligned to sorghum genome v2.0 [] using GMAP (genome mapping and alignment program) [] with 80% identity and 90% coverage threshold to compare between the two genomes. SAMtools v1.2 [] were used to analyse the mapping files., Assemblies were assessed by QUAST program []. All Venn diagrams were created by the online Venn tool []. All analyses using command-line packages were performed at the High Performance Computer clusters, Euramoo, Flashlite and Tinaroo, hosted by Research Computing Center, The University of Queensland, Australia []. The CLC-GWB analyses were conducted on a CLC Genomics Server the CLC server, nodes and CLC-clien […]

Pipeline specifications

Software tools InterProScan, WEGO, KAAS, GHOSTX
Databases PlantTFDB