NCBI CD-Search的本地版安装与使用（windows）

NCBI CD-Search的本地版使用

参考文献 NCBI’s Conserved Domain Database and Tools for Protein Domain Analysis

##NCBI的保守结构域数据库以及蛋白结构域分析工具 重点看RPS-BLAST and rpsbproc部分
https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpbi.90

Basic Protocol 1: CD-search

Basic Protocol 2: Batch CD-search

Basic Protocol 3: Standalone RPS-BLAST and rpsbproc
Standalone“单机版”，应该指的是这些工具可以在没有网络连接的情况下，独立于任何在线服务，在个人计算机或本地服务器上运行的版本。

Use Standalone RPS-BLAST and rpsbproc(https://ftp.ncbi.nih.gov/pub/mmdb/cdd/rpsbproc/e) （这个网址好像失效了）to compute and retrieve（检索） domain annotation programmatically. Basic Protocol 3 demonstrates how to identify protein domains for a batch of protein queries of greater than 4000.演示了如何为超过4000个蛋白质查询序列批量识别鉴定蛋白质结构域。

Hardware硬件配置

An internet-connected Linux, Windows, or Mac workstation
需要一台连接互联网的工作电脑平台，操作系统可以是 Linux、Windows 或 Mac

Software软件要求

• Web browser, for downloading files from FTP site 浏览器，用于从FTP站点下载文件
• The tar utility tar解压工具, to extract files from compressed archive(打包的，指的是包含了一个或多个文件或文件夹的文件的) files: A built-in(内置的）utility for the Linux, Windows, and Mac platforms, found in Shell (Linux), Windows Command Processor (Windows), and Terminal (Mac), respectively. 一个内置于 Linux、Windows 和 Mac 平台的工具，分别在 Linux 的 Shell、Windows 的命令处理器和 Mac 的终端中可以找到
• The gzip utility, required to decompress files: For the Linux and Mac platforms, commonly a built-in utility by default; for the Windows platform, the specified software, including 7-Zip, WinZip, and others, can be used gzip 工具，用于解压文件：对于 Linux 和 Mac 平台，通常默认内置此工具；对于 Windows 平台，需要使用指定的软件，包括 7-Zip、WinZip 等来进行操作。
• The curl utility, for downloading files from FTP site (optional): For the Linux platform, commonly installed by default; for Windows and Mac platforms, can be downloaded from
  (https://curl.haxx.se/download.html) and installed manually curl 工具，用于从 FTP 站点下载文件（可选）：对于 Linux 平台，通常默认安装；对于 Windows 和 Mac 平台，可以从 https://curl.haxx.se/download.html 下载并手动安装。
• Specific FTP software, for downloading files from FTP site more efficiently (optional): e.g., FileZilla 特定的 FTP 软件，用于更高效地从 FTP 站点下载文件（可选）：例如，FileZilla。

Files

Input queries in FASTA format: i.e., protein or nucleotide sequences

Preliminary Steps

Detailed instructions on how to retrieve the RPS-BLAST executable and rpsbproc utility and run them locally can be found in the rpsbproc README file at the CDD FTP site (https://ftp.ncbi.nih.gov/pub/mmdb/cdd/rpsbproc/README).

The standalone RPS-BLAST packaged with the pre-built BLAST executables (“rpsblast” for protein queries and “rpstblastn” for nucleotide queries) is available at the NCBI BLAST FTP site and as part of the NCBI C++ toolkit distribution. Detailed documentation for BLAST at NCBI, including R