Transitions vs Transversions

Transitions_&_Transversions

DNA sub­sti­tu­tion muta­tions are of two types. Tran­si­tions are inter­changes of two-ring puri­nes (A <-> G) or of one-ring pyrim­idi­nes (C <-> T): they there­fore involve bases of sim­i­lar shape. Trans­ver­sions are inter­changes of purine for pyrim­idine bases, which there­fore involve exchange of one-ring and two-ring struc­tures.

Trans­ver­sions are inter­changes of purine for pyrim­idine bases, which there­fore involve exchange of one-ring and two-ring struc­tures.

Although there are twice as many pos­si­ble trans­ver­sions, because of the mol­e­c­u­lar mech­a­nisms by which they are gen­er­at­ed, tran­si­tion muta­tions are gen­er­at­ed at high­er fre­quen­cy  than trans­ver­sions. As well, tran­si­tions are less like­ly to result in amino acid sub­sti­tu­tions (due to “wob­ble”), and are there­fore more like­ly to per­sist as “silent sub­sti­tu­tions” in pop­u­la­tions as sin­gle nucleotide poly­mor­phisms (SNPs).

Transition_mutation

Induc­tion of tran­si­tion muta­tions by spon­ta­neous tau­tomer­ic shifts

In the orig­i­nal dou­ble-strand­ed DNA mol­e­cule, A in the stan­dard (amino) form pairs with T. Dur­ing repli­ca­tion, the two strands sep­a­rate. In the upper dia­gram, T pairs with A as usu­al, which repli­cates the wild-type sequence. In the low­er dia­gram, A has under­gone a tau­tomer­ic shift to the non-stan­dard (imi­no) form A’, which pairs with C. In the next round of repli­ca­tion, the imi­no A’ shifts back to the amino A form, which pairs with T, which again repro­duces the wild-type sequence. Repli­ca­tion of the oth­er strand pairs C with G. By com­par­ison with the orig­i­nal mol­e­cule, the result is a  T -> C muta­tion. A tau­tomer­ic shift in one strand has pro­duced a  tran­si­tion muta­tion in the com­ple­men­tary strand. If the muta­tion occurs in the germline, it will be trans­mit­ted to future gen­er­a­tions.

IMPORTANT: Note that a tau­tomer­ic shift is not itself a muta­tion, but a tran­sient change to an alter­na­tive form of the mol­e­cule.

https://www.mun.ca/biology/scarr/Transitions_vs_Transversions.html

https://www.mun.ca/biology/scarr/Transition_mutations.html

Amplicon Sequencing

 

2016-08-11_220831

Ampli­con sequenc­ing is a high­ly tar­get­ed approach for ana­lyz­ing genet­ic vari­a­tion in speci­fic genomic regions. The ultra-deep sequenc­ing of PCR prod­ucts (ampli­cons) allows effi­cient vari­ant iden­ti­fi­ca­tion and char­ac­ter­i­za­tion. Illu­mi­na ampli­con tech­nol­o­gy uses a pair of oligonu­cleotide probes designed to tar­get and cap­ture regions of inter­est, fol­lowed by next-gen­er­a­tion sequenc­ing (NGS).

Ampli­con sequenc­ing is use­ful for the dis­cov­ery of rare somat­ic muta­tions in com­plex sam­ples (such as tumors mixed with germline DNA). Anoth­er com­mon appli­ca­tion is sequenc­ing the bac­te­ri­al 16S rRNA gene across mul­ti­ple species, a wide­ly used method for phy­logeny and tax­on­o­my stud­ies, par­tic­u­lar­ly in diverse metage­nomics sam­ples.

link:http://www.illumina.com/techniques/sequencing/dna-sequencing/targeted-resequencing/amplicon-sequencing.html

牦牛基因组Scaffold总条数95%的统计

Graph­ic:

scaffold

R source code:

length<-c(50,150,250,350,450,550,650,750,850,950,1050,1150,1250,1350,1450,1550)
number<-c(9,87747,12035,5826,4010,3170,1978,1955,1866,1146,739,690,572,380,295,247)
plot(length,number,type="o",main="牦牛基因组Scaffold总条数95%的统计",sub="制作时间:2016年8月6日-23:37 引文:The yak genome and adaptation to life at high altitude (2012)")

RTMPDump

rtm­p­dump is a toolk­it for RTMP streams. All forms of RTMP are sup­port­ed, includ­ing rtmp://, rtmpt://, rtmpe://, rtmpte://, and rtmps://.

Usage of PuTTY

PuT­TY is a free imple­men­ta­tion of SSH and Tel­net for Win­dows and Unix plat­forms, along with an xterm ter­mi­nal emu­la­tor. It is writ­ten and main­tained pri­mar­i­ly by Simon Tatham.

官网下载地址

  1. putty.exe:图形化连接界面
  2. puttygen.exe:公钥,私钥生成器
  3. pscp.exe:向服务器上传文件,从服务器下载文件