Capillary Automated Footprinting Analysis

While capillary electrophoresis (CE) based sequencers are ubiquitous at most institutions, their application to quantitative nucleic acid structural characterization requires special expertise. We therefore set out to harness the potential of CE for the structural characterization of nucleic acids by quantitative chemical mapping. A major limitation to their adoption for nucleic acid structural analysis is the absence of software that can quantitate the elution trace. The ‘base calling’ algorithms necessary for sequencing are not suitable for quantification of the chemical and enzymatic mapping data necessary for structural analysis. Rather, an algorithm capable of deconvoluting overlapping signal is necessary along with software that transforms and manipulates the mapping data. To take advantage of high throughput CE sequencers, we have developed the experimental protocols and the Capillary Automated Footprinting Analysis (CAFA) software described available here that builds upon tested GE analysis tools. The structural analyses derived from CAFA based analysis will be a valuable addition to genome analyses. <br/><br/>This project includes the following software/data packages: <br/> <ul> <li> <a href="https://simtk.org/frs?group_id=263#pack_395">CAFA for Macintosh </a> : This is the Mac specific version of CAFA </li> <li> <a href="https://simtk.org/frs?group_id=263#pack_362">CAFA for Windows </a> : This is a Windows Standalone Version of CAFA </li> <li> <a href="https://simtk.org/frs?group_id=263#pack_375">CAFA Source </a> : Source Code for CAFA </li> </ul>

尽管基于毛细管电泳（CE）的测序仪在大多数机构中普遍存在，但其在定量核酸结构表征方面的应用却需要特殊的专业技能。因此，我们着手利用毛细管电泳的潜力，通过定量化学图谱来对核酸进行结构表征。其被应用于核酸结构分析的主要限制之一是缺乏能够定量洗脱谱的软件。对于测序所需的“碱基调用”算法并不适用于量化化学和酶学图谱数据，这些数据对于结构分析至关重要。相反，需要一种能够解卷积重叠信号的算法，以及能够转换和处理图谱数据的软件。为了充分利用高通量CE测序仪，我们开发了本处的实验方案和毛细管自动足迹分析（CAFA）软件，该软件基于经过测试的GE分析工具。基于CAFA分析得到的结构分析结果将为基因组分析增添宝贵的价值。

本项目包括以下软件/数据包：

<ul>
<li><a href="https://simtk.org/frs?group_id=263#pack_395">CAFA for Macintosh</a>：这是针对Mac的CAFA特定版本</li>
<li><a href="https://simtk.org/frs?group_id=263#pack_362">CAFA for Windows</a>：这是CAFA的Windows独立版本</li>
<li><a href="https://simtk.org/frs?group_id=263#pack_375">CAFA Source</a>：CAFA的源代码</li>
</ul>