SAFA Footprinting Software

Quantitative analysis of gels from hydroxyl radical footprinting and other structure mapping techniques can provide a great deal of insight into the structural details of RNA molecules. We have developed and implemented a software package (SAFA v1.1) that allows rapid quantification of a footprinting gel. By automating many of the steps involved in gel analysis, we estimate that an entire gel with thousands of bands can be quantified in less than 10 minutes. In general all the automated features have amanual override, such that even difficult or exceptional gels can be analyzed with the package. <br/><br/>This project includes the following software/data packages: <br/> <ul> <li> <a href="https://simtk.org/frs?group_id=69#pack_642">Files cited in Simmons et al </a> : In this folder are files cited in the Simmons et al. paper. Please read the "Read Me Text for Folders" text for further description of the files in the folder. </li> <li> <a href="https://simtk.org/frs?group_id=69#pack_264">SAFA for Mac OSX Standalone </a> : Standalone Application for Macintosh OS X 10.4 (Tiger) </li> <li> <a href="https://simtk.org/frs?group_id=69#pack_263">SAFA for Windows Standalone </a> : Standalone for Microsoft Windows XP </li> <li> <a href="https://simtk.org/frs?group_id=69#pack_265">SAFA Source Code </a> : This is the SAFA Source Code that requires Matlab. If you own a copy of Matlab, you should download this instead of the Standalones as the performance is better. </li> <li> <a href="https://simtk.org/frs?group_id=69#pack_266">SAFA v11 Example Files </a> : A series of input and output files for testing SAFA </li> </ul>

对羟基自由基足迹法及其他结构映射技术所获得凝胶的定量分析，能够为RNA分子结构的细节提供大量洞见。本研究团队已开发并实施了一款软件包（SAFA v1.1），该软件包允许对足迹凝胶进行快速定量。通过自动化凝胶分析中的众多步骤，我们估算整个凝胶中数千个条带可以在不到10分钟内完成定量。总体而言，所有自动化功能均设有手动覆盖选项，以确保即便是复杂或异常的凝胶也能使用本软件包进行分析。本项目包含以下软件/数据包：

<ul>
<li><a href="https://simtk.org/frs?group_id=69#pack_642">Simmons 等人论文中引用的文件</a>：本文件夹包含Simmons等人论文中引用的文件。请阅读“文件夹阅读说明文本”以获取文件夹中文件的进一步描述。</li>
<li><a href="https://simtk.org/frs?group_id=69#pack_264">SAFA for Mac OSX Standalone</a>：适用于Macintosh OS X 10.4（Tiger）的独立应用程序。</li>
<li><a href="https://simtk.org/frs?group_id=69#pack_263">SAFA for Windows Standalone</a>：适用于Microsoft Windows XP的独立版本。</li>
<li><a href="https://simtk.org/frs?group_id=69#pack_265">SAFA Source Code</a>：这是SAFA的源代码，需要Matlab。如果您拥有Matlab副本，应下载此源代码而非独立版本，因为性能更佳。</li>
<li><a href="https://simtk.org/frs?group_id=69#pack_266">SAFA v11 Example Files</a>：用于测试SAFA的一系列输入和输出文件。</li>
</ul>

搜集汇总

背景与挑战

背景概述

SAFA Footprinting Software是一个半自动化足迹分析软件包，用于快速定量RNA分子结构映射技术中的凝胶，能将分析时间从几小时缩短至15分钟以内。该数据集提供了多个版本的软件下载，包括Mac和Windows的独立版本、源代码及示例文件。