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)")

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