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最近了解到的生物信息学技术.

TLHL28 posted @ Wed, 11 Jan 2012 16:43:58 +0800 in 随笔 with tags python kegg , 2660 readers

前段时间写了个脚本抓取基因数据,在这里记录下用到的资源.

KEGG:

Kyoto Encyclopedia of Genes and Genomes

KEGG 是一个生物基因和基因组数据库。由GenomeNet网站(目前由京都大学生物信息学研究中心系维护) 继续维护和提供分析服务.

KEGG 有一点非常好,就是提供了KEGG API。方便研究人员自己写脚本定制数据. PS. KEGG提供了SOAP/REST两种方式.

TogoWS

Intergration of the bioinfomatics web services

由于我前面探索的时候走过了一些弯路,需要用到比较复杂的关系查询. 所以找到了 TogoWS 。

它集合了大部分的生物信息中心的数据包括 NCBIEBIDDBJKEGGPDBj, and CBRC提供了统一的查询接口(API). 使用起来很方便。提供了 SOAP/REST 两种调用方式. 还能返回多种数据格式

 

以下分别是由perl, python, ruby 编写的生物信息学编程工具库. 详细的资料请到官方网站了解.

BioPerl

BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl.

BioPython

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers。

这个库的KEGG模块还很不完善,没有API, 没有KEGG数据格式的分析.

BioRuby

Open source bioinformatics library for Ruby。

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