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Fig. 9 | BMC Genetics

Fig. 9

From: An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench)

Fig. 9

Pipeline for building gene structure models. Drought responsive genes were mapped to sorghum genome using UniGene clusters and TIGR transcripts. Sequences were downloaded as described in the method and were screened for quality using RepeatMasker and SeqClean. These were mapped to genome using e-value cutoff 1e-10. The raw out put was parsed and HSPs were extracted using in-house perl script. Percent identity with ≥80% was used to select the HSPs which were further consolidated along the genomic length of 2000 bp as described in the method. These were converted into GFF3 formats to extract associated genomic region that was aligned to the corresponding transcripts using EXONERATE and Blat to generate gene builds. Known and novel gene builds were classified by intersecting and subtracting the data sets respectively using galaxy genomic interval tool. Gene models were identified by AUGUSTUS and optimized by PASA (Additional file 2: Table S14). Finally, genes were visualized by loading the GFF3 formatted files onto the MySQL DB

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