Time: 11:20 AM
The iPlantTF integrates conserved domain patterns for 103 published transcription factor families in plants. These patterns were manually collected, compiled and curated to guarantee the prediction quality. The back-end prediction module employs InterProScan, a popular protein domain search tool, to search unique domains in the user-submitted sequences, and further screen potential transcription factors by referring to conserved domain patterns of each transcription factor family. In order to provide genome-scale analysis capability, we optimized the InterProScan by trimming its databases only to include relevant domain information, and further optimized the back-end prediction module using parallel computing techniques, which are able to effectively use a 400-core Linux cluster. With these optimizations, the iPlantTF system is able to analyze genome-scale sequences, for example, in one test, the iPlantTF was able to satisfactory analyze the entire Arabidopsis thaliana genome within eight minutes.
The iPlantTF is publicly and freely available at http://plantgrn.noble.org/iPlantTF/.