先看一下语言模型的输出格式 \data\ ngram = ngram = ngram = \-grams: -5.24036 'cause -0.2084827 -4.675221 'em -0.221857 -4.989297 'n -0.05809768 -5.365303 'til -0.1855581 -2.111539 </s> 0.0 - <s> -0.7736475 -1.128404 <unk> -0.8049794 -2.271447 a -0.616…

这算是第二讲了,前面一讲是:Edit Distance编辑距离(NM tag)- sam/bam格式解读进阶 MD是mismatch位置的字符串的表示形式,貌似在call SNP和indel的时候会用到. 当然我这里要说的只是利用它来计算mismatch的个数 MD = line.get_tag('MD') pat = "[0-9]+[ATGC]+" MD_list = re.findall(pat,MD) for i in MD_list: for j in i: if j == '…

实验内容:非IMU模式下DML语句产生的REDO日志内容格式解读 最详细的解读是UPDATE的. 实验环境准备 11G中默认是开启IMU特性的,做此实验需要关闭此特性. alter system set "_in_memory_undo"=false; alter system set "_in_memory_undo"=true;  --实验结束后使用此语句改回使用IMU特性. 修改参数完成后,重启数据库: shutdown immediate; startup;…

创世区块配置文件genesis.json的格式解读 中文网站上关于genesis 的解析大多数都来自于这个Gist:Ethereum private network configuration guide. (github.com),但实际上genesis 中的配置项还有一些其他内容. 首先,genesis.json 是Geth 工具用来创建创世区块以及区块链的配置文件,genesis.json 并不是创世区块本身. 查阅Geth 文档,在Using Geth/ Connecting To Th…

sam格式很精炼,几乎包含了比对的所有信息,我们平常用到的信息很少,但特殊情况下,我们会用到一些较为生僻的信息,关于这些信息sam官方文档的介绍比较精简,直接看估计很难看懂. 今天要介绍的是如何通过bam文件统计比对的indel和mismatch信息 首先要介绍一个非常重要的概念--编辑距离 定义:从字符串a变到字符串b,所需要的最少的操作步骤(插入,删除,更改)为两个字符串之间的编辑距离. (2016年11月17日:增加,有点误导,如果一个插入有两个字符,那编辑距离变了几呢?1还是2?我又验证…

本文介绍 wav 文件格式,主要关注该类格式的结构. 参考: [1] 以一个wav文件为实例分析wav文件格式 ( 2017.04.11 CSDN ) [2] WAV ( Wikipedia ) [3] Ubuntu Linux 查看.编辑.比较二进制文件 ( 2014.4.24 ChinaUnix ) [4] wav文件格式分析与详解 ( 2017.10.12 cnblog ) [5] WAV文件格式解析 ( 2017.04.16 CSDN ) [6] wav音频文件格式解析 ( 2016.0…

1)知识简介--------------------------------------------------------1.1)测序质量值 首先在了解fastq,fasta之前,了解一下什么是质量值.phred软件在对reads进行base calling的时候会给出每一个碱基的质量值,这个质量值的计算与测序预期错误率相关(estimated probability of error): Phred Quality Score     Probability of incorrect bas…

关于n-gram 语言模型,大部分在这篇博客里 记过了,   SRILM 语言模型格式解读 , 其实看完了,ngram的大概用法都比较清楚了, 但是关于平滑算法,一直很模糊,就晓得一个"劫富济贫" ,也不知 回退 ,插值,折扣,平滑,都说的什么东西,模模糊糊的,找了很多资料,还是看官方文档吧,看具体公式,就明白了.   看全部翻译 参考 :   Ngram 折扣平滑算法 ,本文里夹带着自己的一些理解.  本文档翻译自 srilm 手册ngram-discount.7.html NAME…

SRILM是一个建立和使用统计语言模型的开源工具包,从1995年开始由SRI 口语技术与研究实验室(SRI Speech Technology and Research Laboratory)开发,现在仍然不断推出新版本,被广泛应用于语音识别.机器翻译等领域.这个工具包包含一组C++类库.一组进行语言模型训练和应用的可执行程序等.利用它可以非常方便地训练和应用语言模型.给定一组连续的词,调用SRILM提供的接口,可以得到这组词出现的概率. http://www.jianshu.com/p/5b1…

1)blast产生背景 双序列比对可以采用是基于动态规划算法的Needleman-Wunsch(NW)和Smith-Waterman algorithm(SW)算法,虽然精度高,但计算消耗大.当与数据库比对的时候,该算法就显得不切实际.因此TASTA,blast采用启发式算法使得通过大幅度丢失灵敏度来减少运行时间.与FASTA软件相比,blast通过把搜索限制在狭隘的矩阵对角线条带上,来改进FASTA进行数据库搜索的速度. 2)blast的大致原理 blast 程序首先查询query序列的所有子…