Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.

ABSTRACT: Predicting protein domains is essential for understanding a protein's function at the molecular level. However, up till now, there has been no direct and straightforward method for predicting protein domains in species without a reference genome sequence. In this study, we developed a functionality with a set of programs that can predict protein domains directly from genomic sequence data without a reference genome. Using whole genome sequence data, the programming functionality mainly comprised DNA assembly in combination with next-generation sequencing (NGS) assembly methods and traditional methods, peptide prediction and protein domain prediction. The proposed new functionality avoids problems associated with de novo assembly due to micro reads and small single repeats. Furthermore, we

SUBMITTER: Lang T 

PROVIDER: S-EPMC4182558 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature