Oxford Nanopore Technology — MinION

Min­ION is a portable device for mol­e­c­u­lar analy­ses that is dri­ven by nanopore tech­nol­o­gy. It is adapt­able for the analy­sis of DNA, RNA, pro­teins or small mol­e­cules with a straight­for­ward work­flow.

MinION

Scalability

The Min­ION can be run for min­utes or days accord­ing to the exper­i­men­tal need. Users can adjust set­tings like the speed that the DNA pass­es through the nanopore. Prome­thION, which will soon be released into ear­ly access, is designed to be ful­ly scal­able so that users can oper­ate between one or 48 flow cells at any one time.

Long read lengths

The Oxford Nanopore sys­tem process­es the reads that are pre­sent­ed to it rather than gen­er­at­ing speci­fic read lengths. The longest read report­ed by a Min­ION user to date is more than 200Kb, but it can process the spec­trum of read lengths.

身边的算法

  1. windows自带纸牌游戏(NP难)
    对于如何生成一副可被完成的组合,这是一个NP难问题;电脑每次随机生成一副牌,不保证一定有解。所以有时候,纸牌游戏无论如何都完成不了时,可能是这次真的完成不了,而不是你自己的问题。不过,判定到底是你的问题还是电脑的问题仍然是NP难的问题。可以编写一个程序,来算:当我们觉得已经无法前进时,出现了的所有牌,是否存在一种新的组合会使得出现新的翻牌希望。

Keywords of Genomics

Pop­u­la­tion genet­ics

Pop­u­la­tion genet­ics is the study of the dis­tri­b­u­tion and change in fre­quen­cy of alle­les with­in pop­u­la­tions, and as such it sits firm­ly with­in the field of evo­lu­tion­ary biol­o­gy.

The main process­es of evo­lu­tion are nat­u­ral selec­tion, genet­ic drift, gene flow, muta­tion, and genet­ic recom­bi­na­tion and they form an inte­gral part of the the­o­ry that under­pins pop­u­la­tion genet­ics.

Stud­ies in this branch of biol­o­gy exam­ine such phe­nom­e­na as adap­ta­tion, spe­ci­a­tion, pop­u­la­tion sub­di­vi­sion, and pop­u­la­tion struc­ture.

Pop­u­la­tion strat­i­fi­ca­tion

Pop­u­la­tion strat­i­fi­ca­tion refers to dif­fer­ences in allele fre­quen­cies between cas­es and con­trols due to sys­tem­at­ic dif­fer­ences in ances­try rather than asso­ci­a­tion of genes with dis­ease.

It would be caused by sys­tem­at­ic dif­fer­ences in the ances­try of cas­es and con­trols.

Diploid genome

Diploid genome refers to a genome that con­tains a bal­anced set of chro­mo­somes derived equal­ly from mater­nal and pater­nal sources.

Coa­les­cent the­o­ry

Coa­les­cent the­o­ry is a ret­ro­spec­tive sto­chas­tic mod­el of pop­u­la­tion genet­ics that relates genet­ic diver­si­ty in a sam­ple to demo­graph­ic his­to­ry of the pop­u­la­tion from which it was tak­en.

That is, it is a mod­el of the effect of genet­ic drift, viewed back­wards in time, on the geneal­o­gy of antecedents.

GitHub

Repos­i­to­ry

A repos­i­to­ry is usu­al­ly used to orga­nize a sin­gle project. Repos­i­to­ries can con­tain fold­ers and files, images, videos, spread­sheets, and data sets – any­thing your project needs. We rec­om­mend includ­ing a README, or a file with infor­ma­tion about your project. GitHub makes it easy to add one at the same time you cre­ate your new repos­i­to­ry. It also offers oth­er com­mon options such as a license file.

Branch

Branch­ing is the way to work on dif­fer­ent ver­sions of a repos­i­to­ry at one time.

By default your repos­i­to­ry has one branch named mas­ter which is con­sid­ered to be the defin­i­tive branch. We use branch­es to exper­i­ment and make edits before com­mit­ting them to mas­ter.

Com­mit

On GitHub, saved changes are called com­mits.

Pull Request

When you open a pull request, you’re propos­ing your changes and request­ing that some­one review and pull in your con­tri­bu­tion and merge them into their branch. Pull requests show diffs, or dif­fer­ences, of the con­tent from both branch­es. The changes, addi­tions, and sub­trac­tions are shown in green and red.

GitHub Pages

Not­twya

GitHub Pages are pub­lic web­pages host­ed and pub­lished through our site.

You can cre­ate and pub­lish GitHub Pages online using the Auto­mat­ic Page Gen­er­a­tor. If you prefer to work local­ly, you can use the GitHub Desk­top or the com­mand line.

Pages are served over HTTP, not HTTPS, so you shouldn’t use them for sen­si­tive trans­ac­tions, like send­ing pass­words or cred­it card num­bers.

如何读文章?

  1. 读摘要
    通过摘要,我们能快速知道,这篇文章的主题、研究对象和实验结论等,这些能够帮助我们最终确定这篇文章是否含有我们需要的信息;
  2. 读图
    通过读图,我们能够迅速知道这篇文章比较凝练的信息,从而快速切入这篇文章的核心结论;此外,图片方便理解,通过图片能够帮助我们对文章建立初步认识;
  3. 选读
    在进行了上面两步以后,选定自己感兴趣的部分进行深入阅读。

J.Q. Liu

  1. Yak whole-genome rese­quenc­ing reveals domes­ti­ca­tion sig­na­tures and pre­his­toric pop­u­la­tion expan­sions (2015)
    1. genome vari­a­tion of wild and domes­tic yaks
    2. evo­lu­tion
  2. Genome rese­quenc­ing: 13 wild yaks and 59 domes­tic yaks

windows install and configure

如果是让电脑维修店的人重装系统,要注意找一家好一点的维修店。因为,重装系统看似一样,其实,每个店使用的安装镜像以及一些细节的配置是有出入的。去一家很差的店,重装的系统,会给自己后期的配置带来极大的困难。

  1. 操作系统重装
    win7
  2. 硬件驱动重装
    1.显卡驱动
  3. 软件重装
    1. Direc­tX
  4. 运行库
  5. 编程语言编译工具
    1. Java
    2. MinGW
    3. Straw­ber­ry Perl
  6. 小工具
    1. dae­mon tool lites
    2. pchunter
    3. xming+putty
  7. 123

NCBI 使用注意事项及技巧

  1. 关于序列标识join和complement:
    join:表示序列是模板链上的5'->3';
    complement:表示序列是编码链上的5'->3';
    example:
    join:
    现在(2016.4.5),似乎没有再标识join了。
    complement:
    我看到的素有gene类别下的序列都是给的complement。

    gene complement(2872..3195)
    /gene=" lacZ' "
    Sequence:NC_000913.3 (363231..366305, complement)

  2. 在指定的基因组检索目的序列:打开基因组,然后输入目的序列,开始检索。
  3. 对于蛋白质,NCBI提供了查看其CD(conserved domain),名字叫“Identify Conserved Domains”;

WordPress 建站配置

  1. 连接数据库
    1. 在空间提供商处找到数据库的IP;
    2. 在网站根目录下找到WP的wp-config.php文件;
    3. 将DB_HOST的值,改为数据库的IP
  2. 备份
    1. 使用WP自带的工具中的导出工具,导出能被WP模板普遍识别的网站内容,方便在网站出现意外时,在任何一个新的WP木板上导入网站所有内容(不含图片)。
    2. 使用空间提供商的数据下载,直接下载整个网站,如若网站出现问题,直接从新上传整个WP;
  3. 防垃圾评论
    1. WP自身会要求管理者审核每一条评论;
    2. 使用Akismet,以后会自动过滤同一个邮箱的评论;

Windows 10系统故障修复和优化配置集锦

  1. 开机蓝屏,出现“BAD_SYSTEM_CONFIG_INFO”:(windows 10)
    1. 选择“高级修复-疑难解答-命令提示符”
    2. 执行命令:“bcdedit /deletevalue {default} truncatememory
  2. 运行时蓝屏,出现:
    1. video memory management internal: 安装合适的显卡驱动
    2. VIDEO TDR FAILURE (nvlddmkm.sys)
    3.video scheduler internal error
  3. 出现蓝屏死机(Blue screen of death)时,系统自动记录DMP文件所在位置(win-10):c:/Windows/Minidump/
  4. IE浏览器打不开网页(windows 7)
    1. 选择“Internet选项-高级”
    2. 在“重置Internet Explorer设置”处,点击重置
  5. DLL
    1. 安装:Visual C++ Redistributable Packages for Visual Studio 2013,msvcp120.dll,Microsoft Visual C++ 2010 可再发行组件包 (x86)
  6. 无法指定一个电脑上存在的软件为默认打开程序
    1. 打开注册表编辑器;(cmd->regedit);
    2. 到达该位置:HKEY_CURRENT_USER\Software\Classes\Applications
    3. 检查该软件是否存在,不存在则添加;检查该软件路径是否正确,不正确则修改正确路径。
  7. 系统和压缩内存占用内存过高
    0. cmd -> regedit;
    1. HKEY_LOCAL_MACHINE\SYSTEM\ControlSet001\Control\Session  Manager\Memory Management\PrefetchParameters
    2. 将“EnablePrefetcher”和“EnableSuperfetch”的值调为2;
    3. 重启;
    备注:
    值-2 :开启系统启动预读取
    值-3 :开启应用启动和系统启动预读取
  8. win10-关闭Cortana
    1. 点击启动按钮;
    2. 点击设置->隐私->语音、墨迹书写和键入;
    3. 点击,停止搜集有关我的信息;
  9. win10-关闭windows search
    1. 控制面板->管理工具->服务;
    2. 禁用windows search。
  10. win10-禁止自动更新
    1. gpedit.msc
    2. 计算机配置—管理模板—Windows组件-Windows更新
    3. “配置自动更新”,“2 = 在下载和安装任何更新前发出通知”
  11. Itunes: error 7 (windows error 193)
    当我们从win7升级到win10以后,可能会出现这个软件无法卸载,并且新的itune不能安装。这个时候怎么办呢?就得使用微软专门开发的工具: MicrosoftProgram_Install_and_Uninstall.meta.diagcab。
    运行这个软件,卸载掉apple software update,之后就可以顺利安装itunes了。
    微软的两个帖子,如何解决 Windows installer 服务的问题修复阻止程序安装或删除的问题
  12. 接入需要验证的拨号网络时,会自动打开浏览器并连接这个网址:http://go.microsoft.com/fwlink/?LinkID=219472&clcid=0x409
    1. sfc/scannow (windows+x,命令提示符-管理员)
    What is the Sfc Command?
    The sfc command is a Command Prompt command that can be used to verify and replace important Windows system files.
    System File Checker is a very useful tool to use when you suspect issues with protected Windows files like many DLL files.
    Sfc /scannow will inspect all of the important Windows files on your computer, including Windows DLL files. If System File Checker finds an issue with any of these protected files, it will replace it.
    2. run:

    findstr /c:"[SR] Cannot repair member file" %windir%\logs\cbs\cbs.log > "%userprofile%"\Desktop\sfcdetails.txt

    3. correct the error according to the information given in the file "Desktop\sfcdetails.txt";

  13. 通过防火墙禁止应用程序联网:
    1. win+x;
    2.控制面板,小图标,windows防火墙;
    3.高级设置,入战规则,新建规则;
    4.程序,此程序路径,阻止连接。
    caveat:一定要在公用网络和专用网络下都打开windows防火墙,方法:到达上面第2步后,点击“启用或关闭windows防火墙”,打开两个网络下的防火墙。
  14. 右下角小图标收拢
    1.点击左下角图标,点击设置,点击系统
    2.点击通知和操作
    3.选择在任务栏上显示哪些图标
    4.关闭“通知区域始终显示所有图标”
  15. 清除右键多余项:
    1.  win+r
    2. regedit, 回车;
    3.  编辑,搜索需要删除的项目
    4. (如果需要删除的项目,是已经卸载的软件)删掉所有搜索出来的结果。(更可能是hkey-local-machine下的)补充信息:
    reg_sz:A null-terminated string. This will be either a Unicode or an ANSI string, depending on whether you use the Unicode or ANSI functions.
  16. chm打开后空白
    右键->属性->勾选:解除锁定
  17. 开启管理员账户状态:
    1. cmd: gpedit.msc
    2. Windows 设置 -> 安全设置 -> 本地策略 -> 安全选项,找到“账户:管理员账户状态”
    3. 右键,属性,修改为已启用。
  18. 禁止计算机进入睡眠和休眠:
    比较容易达到的是禁止计算机睡眠,但是禁止计算机休眠的选项在很深的位置,这样一来,计算机长时间(我的是3小时)不用以后,就会进入休眠,这会给远程控制带来很大的麻烦。改变这个设置的具体操作流程如下:
    1. win+i,启动设置界面
    2. 系统->电源和睡眠->其他电源设置->更改计算机睡眠时间->更改高级电源设置->睡眠->在此时间后休眠
    3. “接通电源”选项后面的框内,选择:从不。
  19. foobar

五分法-如何读书或者文章

从Pod­cast-清华大学广播台-珊越拾穗–读书小贴士里听到的,觉得很有用。特此记录下来,不断加深巩固理解。

如何读书

  1. 历史化(historicize)
    了解这个书或者文章产生的背景。
  2. 对话式(dialogue)
    看一本书时,要有一个跟这本书相反意见的或者跟他相似意见的书,同时去看。看别的作家怎么讨论这个问题。然后就会发现作家的风格不同,读起来感觉不同。另外是读者跟作者的对话。
  3. 智性化(intellectualize)
    从读书过程中找到、发展自己的观点。
  4. 转化(transformative)
    通过阅读,有自己的发现和创新。

读文章

  1. 找到作者想要回答的问题
    作者通过写这本书,这篇文献,想要解决什么问题。
  2. 他有表述哪些竞争性的理论
    一个研究不可能是开天辟地,头一个的研究。这个问题肯定之前有被研究过,或者其他理论可以解释这个问题。在作者的作品中,他使用了哪些人的理论来解释这个问题,他是怎么解释的,这些理论在解释这个问题中是否有什么不足。
  3. 作者提出了他自己的什么观点
    除了前人的理论,他自己对这个问题的解读。
  4. 他用了什么东西,什么样的步骤,什么数据证明自己
    他是怎么证明自己的观点的。
  5. 他的长处和不足
    讨论他的文章的长处和不足。

写文章

  1. 我要解答什么问题;
  2. 别人是怎么解答这个问题的;
  3. 我和别人有什么不一样;
  4. 我怎么证明这个不一样是站得住脚的;
  5. 那我有什么不足或者我有什么新的发现或者我有什么优点。

特此向主播的导师,总结出这个方法的人,致以我的敬意。

TED speaker

Benoit Man­del­brot: (20 Novem­ber 1924 – 14 Octo­ber 2010)

TED title: Frac­tals and the rough­ness
Intro­duc­tion:  Benoit Man­del­brot was a Pol­ish-born, French and Amer­i­can math­e­mati­cian. He is rec­og­nized for his con­tri­bu­tion to the field of frac­tal geom­e­try, which includ­ed coin­ing the word “frac­tal” as well as for devel­op­ing a “the­o­ry of rough­ness” and “self-sim­i­lar­i­ty” in nature.

Carter Emmart

TED title: A 3D atlas of the uni­verse
Intro­duc­tion: It is a stand­alone 4-dimen­sion­al space visu­al­iza­tion appli­ca­tion built on the pro­gram­ma­ble Partiview data visu­al­iza­tion engine designed by Stu­art Levy of the Nation­al Cen­ter for Super­com­put­ing Appli­ca­tions (NCSA) as an adjunct of the NCSA’s Vir­tu­al Direc­tor vir­tu­al chore­og­ra­phy project. The Vir­tu­al Uni­verse Atlas project was launched by the Amer­i­can Muse­um of Nat­u­ral History’s Hay­den Plan­e­tar­i­um with sig­nif­i­cant pro­gram­ming sup­port from the Nation­al Aero­nau­tics and Space Admin­is­tra­tion as well as Stu­art Levy. The data­base draws on the Nation­al Vir­tu­al Obser­va­to­ry.

Daniel Kah­ne­man

TED title: The rid­dle of expe­ri­ence vs. mem­o­ry.
Intro­duc­tion: (Hebrew: דניאל כהנמן‎, born March 5, 1934) is an Israeli-Amer­i­can psy­chol­o­gist notable for his work on the psy­chol­o­gy of judg­ment and deci­sion-mak­ing, as well as behav­ioral eco­nom­ics, for which he was award­ed the 2002 Nobel Memo­ri­al Prize in Eco­nom­ic Sci­ences (shared with Ver­non L. Smith). His empir­i­cal find­ings chal­lenge the assump­tion of human ratio­nal­i­ty pre­vail­ing in mod­ern eco­nom­ic the­o­ry.

python 使用技巧

  1. 安装 pip:
    1. 下载:https://bootstrap.pypa.io/get-pip.py
    2. 安装:python get-pip.py
  2. 在win­dows下使用pip:
    python –m pip
  3. error:Microsoft Visu­al C++ 9.0 required(Unable to find vcvarsall.bat).
    解决方法:下载 VCForPython27.msi 。
    地址: http://www.microsoft.com/en-us/download/confirmation.aspx?id=44266

虞美人

C130720

break

break

少年听雨歌楼上,
红烛昏罗帐。
去年听雨客舟中,
江阔云低,
断雁叫西风。

而今听雨屋檐下,
秋叶已凋零。
悲欢离合总多情,
伊人何处?
总在寒冷清秋。

2132454423561438277

Basic information on S.suis

  1. one of the most preva­lent pathogens in swine caus­ing a range of dis­ease syn­dromes includ­ing arthri­tis (关节炎), menin­gi­tis (脑膜炎), pneu­mo­nia (肺炎), sep­ticemia (败血症) and endo­cardi­tis (心内膜炎), etc. [1]
  2. an zoonotic agent able to induce menin­gi­tis, endo­cardi­tis, and strep­to­coc­cal tox­ic shock-like syn­drome in humans. [1]
  3. Thir­ty three S. Suis serotypes iden­ti­fied on the basis of anti­genic dif­fer­ences in their CPS (Cap­sule Poly­sacharides). [1]
  4. S. suis 2 main­ly infects peo­ple who have direct con­tact with car­ri­er pigs, sick pigs, or raw pork via wounds on the skin, or the mucosa of the mouth, or nasal cav­i­ty. [1]
  5. 1642 cas­es of S. suis human infec­tion had been report­ed world­wide until Dec. 31, 2013. [1]

[1]. Zhang, Y., Ding, D., Liu, M., Yang, X., Zong, B., Wang, X., Chen, H., Bei, W., and Tan, C. (2016). Effect of the gly­co­syl­trans­feras­es on the cap­su­lar poly­sac­cha­ride syn­the­sis of Strep­to­coc­cus suis serotype 2. Micro­bi­o­log­i­cal research.

The elements for building a website — 建站必备

  1. Domain name — 域名
    功能:让对方找到你的网站。
    购买处:西部数码
  2. Web host­ing — 主机托管
    功能:放置你的网站主体(包括,文字、图像、声音、脚本等)的地方。
    购买处:hostinger
  3. File man­ager
    功能:网站文件的上传、下载和修改
    推荐:FileZilla
  4.  Raster graph­ics edi­tor
    功能:图片编辑
    推荐:photoshop
  5. Browser
    功能:网页效果预览
    推荐:Google Chrome、Firefox
  6. CMS (Con­tent Man­age­ment Sys­tem)
    功能:方便用户管理网站内容,发布内容;
    推荐:WordPress

Key points of the analysis of microarray — 基因芯片分析要点

  1. bio­log­i­cal repli­cates — 生物学重复
    Five or more is usu­al­ly robust for micro-array stud­ies
    五个及以上的样本数对基因芯片研究来说才是具有鲁棒性的。
  2. qPCR val­i­da­tion
    Micro-array may give many false pos­i­tives so it is usu­al­ly nec­es­sary to val­i­date the dif­fer­en­tial expres­sion observed in some of the key genes.
    基因芯片可能产生许多的假阳性结果,所以验证部分关键的差异表达基因通常来说是必须的。

Effect of the glycosyltransferases [糖基转移酶] on the CPS [荚膜多糖] synthesis of S.suis 2

  1. The incom­plete CPS result­ing from dele­tion of the cps genes in S.suis 2 SC19;
  2. Inter­play between S.suis 2 SC19 and dif­fer­ent cell lines in vit­ro changed by the­se
    genes dele­tion
    cps2E, cps2G, cps2J and cps2L
  3. More depo­si­tion on the mutant strains of com­ple­ment C3 in porcine serum
    than on WT
  4. Essen­tial role of the cps genes in via­bil­i­ty of SC19 in a murine mod­el

Zhang, Y., Ding, D., Liu, M., Yang, X., Zong, B., Wang, X., Chen, H., Bei, W., and Tan, C. (2016). Effect of the gly­co­syl­trans­feras­es on the cap­su­lar poly­sac­cha­ride syn­the­sis of Strep­to­coc­cus suis serotype 2. Micro­bi­o­log­i­cal research.

LaTeX 随笔

  1. LaTeX在windows下认识的文件路径是“/”,而使用Perl的File::Spec包得到的路径使用的是“\”;
  2. 生成d­vi: latex filename.tex;
  3. 生成pdf: dvipdfm filename.dvi;

KEGG 使用注意事项

  1. bta里的pathway个数在不断增加,过去抓取的和现在的混着用就会出错;
  2. 批量下载KEGG Mapper生成的图像时,由于网络状况可能导致下载不完全,请一定仔细核实数目是否对应,图像是否完整;

KEGG ORTHOLOGY (KO) Database

在KEGG中,分子水平上的功能保存在KO(KEGG Orthology)数据库中。这些功能与直系同源组联系在一起,以此来使得一个特殊物种的实验数据可以被扩展到其他物种。KEGG中的基因组注释是直系同源注释,其方式为,为GENES数据库中的每个基因制定KO iden­ti­fiers (K num­bers) 。对于原始数据,像由RefSeq或者GenBank给出的基因名和描述,即使他们和KO的分配不一致,KEGG也不会做任何修改。

将KO的条目与功能表征的序列数据的实验证据联系在一起的工作,已经开始了,并且现在已经展示在REFERENCE下的SEQUENCE子域中。而且,基因组层面的“KEGG GENES”(http://www.genome.jp/kegg/genes.html)集合已经被扩展,使其可以将蛋白数据也包含在附录中。最终KO数据库将覆盖所有的功能表征蛋白序列信息(另见“KEGG Enzyme”(http://www.genome.jp/kegg/annotation/enzyme.html))。

In KEGG, mol­e­c­u­lar-lev­el func­tions are stored in the KO (KEGG Orthol­o­gy) data­base and asso­ci­at­ed with ortholog groups in order to enable exten­sion of exper­i­men­tal evi­dence in a speci­fic organ­ism to oth­er organ­isms. Genome anno­ta­tion in KEGG is ortholog anno­taion, assign­ing KO iden­ti­fiers (K num­bers) to indi­vid­u­al genes in the GENES data­base. No updates are made to orig­i­nal data, such as gene names and descrip­tions given by Ref­Seq or Gen­Bank, even if they are incon­sis­tent with the KO assign­ment.

Major efforts have been ini­tat­ed to asso­ciate each KO entry with exper­i­men­tal evi­dence of func­tion­al­ly char­ac­ter­ized sequence data, now shown in the SEQUENCE sub­field of the REFERENCE field. Fur­ther­more, the genome-based col­lec­tion of KEGG GENES has been expand­ed to allow indi­vid­u­al pro­tein data to be includ­ed in the adden­dum cat­e­go­ry. Even­tu­al­ly the KO data­base will cov­er all knowl­edge on func­tion­al­ly char­ac­ter­ized pro­tein sequences (see also KEGG Enzyme).

一般来说,KO对功能直系同源的划分是定义在KEGG分子网络的语境中(KEGG path­way maps, BRITE hier­ar­chies and KEGG modules)。KEGG分子网络实际上是由K numbers标识的网络节点表示的。KOs和相应的分子网络的关系呗存储在下面这个系统中。

KEGG Orthol­o­gy (KO

将功能信息和直系同源组关联在一起这个功能是KEGG资源的一个独特的功能。基于有限总量的实验数据生成的对序列相似性的预测被预先定义好在KEGG中。如同在BlastKOALA和其他工具中实现的那样,对KEGG GENES的序列相似性搜索是针对K numbers的。一旦一个K numbers被指定给基因组中的基因,KEGG path­ways maps, Brite hierarchies,和KEGG modules都会自动重建。如此一来,就能对较高水平的功能有一个生物学上的科学的诠释。

In gen­er­al KO group­ing of func­tion­al orthologs is defined in the con­text of KEGG mol­e­c­u­lar net­works (KEGG path­way maps, BRITE hier­ar­chies and KEGG mod­ules), which are in fact rep­re­sent­ed as net­works of nodes iden­ti­fied by K num­bers. The rela­tion­ships between KOs and cor­re­spond­ing mol­e­c­u­lar net­works are rep­re­sent­ed in the fol­low­ing KO sys­tem.

KEGG Orthol­o­gy (KO)The fact that func­tion­al infor­ma­tion is asso­ci­at­ed with ortholog groups is a unique aspect of the KEGG resource. The sequence sim­i­lar­i­ty based infer­ence as a gen­er­al­iza­tion of lim­it­ed amount of exper­i­men­tal evi­dence is pre­de­fined in KEGG. As imple­ment­ed in BlastKOALA and oth­er tools, the sequence sim­i­lar­i­ty search again­st KEGG GENES is a search for most appro­pri­ate K num­bers. Once K num­bers are assigned to genes in the genome, the KEGG path­ways maps, Brite hier­ar­chies, and KEGG mod­ules are auto­mat­i­cal­ly recon­struct­ed, enabling bio­log­i­cal inter­pre­ta­tion of high-lev­el func­tions.