To facilitate the analysis of large-scale high-throughput CE data, we previously proposed a suite of robust and efficient analysis software named HiTRACE (Yoon et al., Bioinformatics, vol. 27, no. 13, pp. 17980- 1805, 2011). It has been intensively used for quantitating data for RNA and DNA based on the mutate-and-map methodology, chromatin footprinting, and other high-throughput structure mapping techniques. However, HiTRACE is based on command-line MATLAB scripts and requires nontrivial efforts to learn, use and extend. Here we present an online version of HiTRACE that presents both standard features previously available only in the MATLAB environment as well as additional features such as automated band annotation and flexible adjustment of annotations, all via an integrative, user-friendly, and interactive environment. By making use of parallelization, the on-line software is also faster than MATLAB implementations available to most users on their local computers.
The flowchart of HiTRACE-Web analysis pipeline is as follows (each of the steps marked with an asterisk corresponds to a tab in the `Analaysis' menu):
The first stage is preprocessing in which the user can select the signal and the reference channels, specify proper regions for analysis, and adjust the baseline. HiTRACE-Web carries out profile alignment in the second stage. Both linear (for within-batch and between-batch alignment) and piece-wise-linear alignment is performed. After alignment, the user can check the intermediate result, provide sequence and structure information, and specify types of chemical reagents in the third stage. In the next stage, HiTRACE-Web provides an automated band annotation functionality, which allows users to complete initial assignments of hundreds of bands in hundreds of profiles in the order of seconds. HiTRACE-Web then performs peak fitting to approximate a profile as a sum of Gaussian curves.
If you have any questions, bug reports, or suggestions regarding HiTRACE, please do not hesitate to contact us: