Category Archives: 生物信息

介绍生物信息学相关知识及其软件的使用

4月 18

在Windows中高效处理文本数据

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  1. GNU utilities for Win32

    2. Here are some ports of common GNU utilities to native Win32. In this context, native means the executables do only depend on the Microsoft C-runtime (msvcrt.dll) and not an emulation layer like that provided by Cygwin tools.
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  2. CoreUtils for Windows

    3. The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.
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    下载：EXE；BIN

  3. Time For Science中的部分PELR2EXE

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3月 30

在R中调用igraph绘制网络图

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  1. igraph简介

    2. igraph is a free software package for creating and manipulating undirected and directed graphs. It includes implementations for classic graph theory problems like minimum spanning trees and network flow, and also implements algorithms for some recent network analysis methods, like community structure search.……【阅读全文】

3月 26

基因组的坐标系统：0-based与1-based

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在现实生活中，我们经常会遇到从0开始计数还是从1开始计数的问题。此处先从现实生活中的实例说起，过渡到电脑编程，然后再详细解释基因组的坐标问题，最后列出一些有用的网址，感兴趣的可以继续阅读、加深理解。

  • first floor的问题

In British English the floor of a building at street level is the ground floor and the floor above that is the first floor.
在英式英语中, 楼房地面与街道相平的楼层叫ground floor, ground floor上面的一层叫first floor.

In US English the street-level floor is the first floor and the one above is the second floor.
在美式英语中, 与街道相平的楼层叫first floor, 其上面的一层叫second floor.
注：以上解释来源于《牛津英汉双解美化版》。
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3月 26

使用BioPerl解析BLAST结果

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虽然有多种多样的办法来解析BLAST，即时单单对于Perl/BioPerl来说，你可以找到好多已有的脚本，如：blast_parsing.pl。但要想灵活的控制筛选条件及输出结果，还需要自己撰写脚本或者修改别人的脚本。所有这些的前提是你对BLAST结果中的各个项目有所了解，同时要知道如何提取出自己想要的项目。……【阅读全文】

3月 10

biopieces：生物信息学数据处理的瑞士军刀

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  • 简介（摘自官网）

The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services. The Biopieces are executed in a command line environment where the data stream is initialized by specific Biopieces which read data from files, databases, or web services, and output records to the data stream that is passed to downstream Biopieces until the data stream is terminated at the end of the analysis.……【阅读全文】