Reverse complement DNA

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用法:python rev_comp.py input.fa out.fa 输入文件为 fasta 格式文件,若输入文件中序列的 header 有 '+' 或 '-' 号标记正负链,则带有 '+' 的序列保持不变,带有 '-' 的序列反向互补: 若 header 没有 '+' 或 '-' 号标记, 则默认按反义链处理. cat input.fa >seq1 + AGATAGATGAATT >seq2 - GATAGAGAATAAA AGATATAGATAGA >seq3 GAATATAT…

3.Complementing a Strand of DNA

Problem In DNA strings, symbols 'A' and 'T' are complements of each other, as are 'C' and 'G'. The reverse complement of a DNA string ss is the string scsc formed by reversing the symbols of ss, then taking the complement of each symbol (e.g., the re…

03 Complementing a Strand of DNA

Problem In DNA strings, symbols 'A' and 'T' are complements of each other, as are 'C' and 'G'. The reverse complement of a DNA string ss is the string scsc formed by reversing the symbols of ss, then taking the complement of each symbol (e.g., the re…

为什么Erlang比C慢那么多倍？

Erlang 一直以慢“著称”,本文就来看看 Erlang 慢在什么地方,为什么比实现同样功能的 C 语言程序慢那么多倍.Erlang 作为一种虚拟机解释的语言,慢是当然的.不过本文从细节上分析为什么 Erlang 这种虚拟机语言会慢. 本文从 shootout benchmark[注1]中选择了一个 Erlang 和 C 语言单核性能差距最大的例子——reverse complement[注2].根据 shootout 网站上给出的使用某款 64 位处理器单个核心的 benchmark 数据,…

het smooth 组装高杂合度二倍体基因组前期数据处理

http://sourceforge.net/projects/het-smooth/ equencing technologies, such as Illumina sequencing, provide the sequences ofshort "reads" of DNA that come from random positions on the genome. These readsthen must be assembled de-novo into the origi…

biopython

转载Part 2 Biopython的重头戏-生物学中序列的处理 Biopyhton的Seq和Python中标准字符串有两大重要的不同之处:首先,他们的处理方法不同.Seq适用于很多不同字符串的用的方法,如translate(),但是又有所不同.而且Biopython中加入了不同字符处理中没有的方法,如reverse_complement(); 第二,Seq模块中加入了重要的特性alphabet,这个对象可以解释序列代表的意思,即这个序列是一个DNA序列还是蛋白质序等. 是alphabet对象…

08 Translating RNA into Protein

Problem The 20 commonly occurring amino acids are abbreviated by using 20 letters from the English alphabet (all letters except for B, J, O, U, X, and Z). Protein strings are constructed from these 20 symbols. Henceforth, the term genetic string will…