title: HiTRACE: high-throughput robust analysis for capillary electrophoresis.
abstract: BACKGROUND
  Capillary electrophoresis (CE) of nucleic acids is a workhorse technology underlying high-throughput genome analysis and large-scale chemical mapping for nucleic acid structural inference. Despite the wide availability of CE-based instruments, there remain challenges in leveraging their full power for quantitative analysis of RNA and DNA structure, thermodynamics and kinetics. In particular, the slow rate and poor automation of available analysis tools have bottlenecked a new generation of studies involving hundreds of CE profiles per experiment.
  
  
  RESULTS
  We propose a computational method called high-throughput robust analysis for capillary electrophoresis (HiTRACE) to automate the key tasks in large-scale nucleic acid CE analysis, including the profile alignment that has heretofore been a rate-limiting step in the highest throughput experiments. We illustrate the application of HiTRACE on 13 datasets representing 4 different RNAs, 3 chemical modification strategies and up to 480 single mutant variants; the largest datasets each include 87 360 bands. By applying a series of robust dynamic programming algorithms, HiTRACE outperforms prior tools in terms of alignment and fitting quality, as assessed by measures including the correlation between quantified band intensities between replicate datasets. Furthermore, while the smallest of these datasets required 7-10 h of manual intervention using prior approaches, HiTRACE quantitation of even the largest datasets herein was achieved in 3-12 min. The HiTRACE method, therefore, resolves a critical barrier to the efficient and accurate analysis of nucleic acid structure in experiments involving tens of thousands of electrophoretic bands.
authors.affiliation: School of Electrical Engineering, Korea University, Seoul 136-713, Republic of Korea. sryoon@korea.ac.kr
authors.forename: Sungroh
authors.initials: S
authors.lastname: Yoon
authors.forename: Jinkyu
authors.initials: J
authors.lastname: Kim
authors.forename: Justine
authors.initials: J
authors.lastname: Hum
authors.forename: Hanjoo
authors.initials: H
authors.lastname: Kim
authors.forename: Seunghyun
authors.initials: S
authors.lastname: Park
authors.forename: Wipapat
authors.initials: W
authors.lastname: Kladwang
authors.forename: Rhiju
authors.initials: R
authors.lastname: Das
mesh_terms: D000465:Algorithms; D019075:Electrophoresis, Capillary / Q000379:methods*; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA
chemical_list: D009696:Nucleic Acids