(Panda, dog and human repeat comparison):与其他动物比较重复序列 我们使用Repbase 库(重复序列库)+已知的转录原件序列+识别软件,评估出转录原件占比,并且与狗和人相比.用Repbase数据库(扩张度来自repeat base)分析熊猫基因中的转录原件的扩张度,得到:大部分熊猫转录原件基因有超过10% 的共有序列的扩张度(这是因为repbase数据库数据基于哺乳动物基因,并没有大熊猫基因).小部分低于10%的扩张度(这可能是哺乳动物最近起源的活性转座…

Multiple sequence alignment Benchmark Data set 1. 汇总: 序列比对标准数据集: http://www.drive5.com/bench/ This is a collection of multiple alignment benchmarks in a uniform format that is convenient for further analysis. All files are in FASTA format, with upper…

本系列介绍几种序列对齐方法,包括Dynamic time warping (DTW),Smith–Waterman algorithm,Cross-recurrence plot Dynamic time warping (DTW) is a well-known technique to find an optimal alignment between two given (time-dependent) sequences under certain restrictions. ——Mei…

A recurrence plot (RP) is a straightforward way to visualize characteristics of similar system states attained at different times (Eckmann et al., 1987).  ,即RP可识别在时间上伸缩的状态对.Cross-Recurrent Plot,形成一个二维坐标轴,坐标系里的黑色代表相似的状态对,实际上在这个坐标系里,大部分的点都不是黑色的.在对角线上的路…

Smith–Waterman algorithm 首先需要澄清一个事实,Smith–Waterman algorithm是求两个序列的最佳subsequence匹配,与之对应的算法但是求两个序列整体匹配的算法是Needleman-Wusch algorithm,即 Smith–Waterman algorithm:Local Needleman-Wusch algorithm: Global Needleman-Wusch algorithm与longest common subsequence…

sequencing:使用二代测序原因:高通量,短序列 不用长序列原因: 1.算法错误率高 2.长序列测序将嵌合体基因错误积累.嵌合体基因:通过重组由来源与功能不同的基因序列剪接而形成的杂合基因 sequencing: 增多的total length>N>gap>missing in genome The reads with a frequency > 1 were called duplicated reads, and we defined the duplication r…

使用IDENTITY列属性 1. 建立表 Sales.MyOrders USE TSQL2012; IF OBJECT_ID(N'Sales.MyOrders', N'U') IS NOT NULL DROP TABLE Sales.MyOrders; GO CREATE TABLE Sales.MyOrders ( orderid , 1) CONSTRAINT PK_MyOrders_orderid PRIMARY KEY, custid INT NOT NULL ), empid INT…

Learn what’s included in Prism 5.0 including the documentation, WPF code samples, and libraries. Additionally find out where to get the library and sample source code and the library NuGet packages. Prism5.0中包含了文档,WPF代码示例,程序集.本篇告诉你从哪里获取程序集和代码示例,还有NuG…

1. For the Impatient # Download bwakit (or from <http://sourceforge.net/projects/bio-bwa/files/bwakit/> manually) wget -O- http://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.15_x64-linux.tar.bz2/download \ | gzip -dc | tar xf - # Genera…

[怪毛匠子 整理] samtools学习及使用范例,以及官方文档详解 #第一步:把sam文件转换成bam文件,我们得到map.bam文件 system"samtools view -bS map.sam > map.bam"; #第二步:sort 一下 BAM 文件,得到map.sorted.bam system"samtools sort map.b/am map.sorted"; #第三步:创建一个关于bam的索引文件,我们得到一个map.sorted.b…