Abstract
In recent research, to analyze the ChIP (chromatin immunoprecipitation) data, many algorithms and computer tools have been developed. Since these programs are developed by academic institutes independently, the lack of common standard makes the talks between them difficult. In this paper, we developed a software system based on workflow for ChIP data analysis, namely CTW (ChIP-Tool-Workflow). CTW is a java-based software platform, which provides a common development interface to integrate data and programs. At the moment, many data types and tools abstracted from CisGenome, MAT and QuEST are integrated. CTW is designed to meet all basic needs of ChIP data analyses, including visualization, data normalization, peak detection, false discovery rate computation, gene-peak association, and sequence and motif analysis. Because the interface developed is very general and flexible, new analysis tools can be integrated effectively as required. CTW implies an ideal environment for integrative Biological research.
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