sequenced plant genomes

A list of sequenced plant genomes

(periodically updated)

https://genomevolution.org/wiki/index.php/Sequenced_plant_genomes

KO, KD, Knockin

gene knockdown
http://en.wikipedia.org/wiki/Gene_knockdown

gene knockout
http://en.wikipedia.org/wiki/Gene_knockout

gene knockin
http://en.wikipedia.org/wiki/Gene_knockin

bim, bam, ngsfse2?

files produced by FusionMap.
unclear about what they are (bim, ngsfse2).
for later processing ....


https://www.biostars.org/p/15608/

http://en.wikipedia.org/wiki/Building_information_modeling

http://www.autodesk.com/solutions/building-information-modeling/overview

http://www.arrayserver.com/wiki/index.php?title=SummaryType

perl heredoc

http://perl.about.com/od/perltutorials/qt/perlheredoc.htm






http://perldoc.perl.org/perlop.html#%3C%3CEOF

Ti/Tv

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.

    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).

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

---

Transition to Transversion Ratio 

Human mutations don't occur randomly. In fact, transitions (changes from A <-> G and C <-> T) are expected to occur twice as frequently as transversions (changes from A <-> C, A <-> T, G <-> C or G <-> T). Thus, another useful diagnostic is the ratio of transitions to transversions in a particular set of SNP calls. This ratio is often evaluated separately for previously discovered and novel SNPs.

Across the entire genome the ratio of transitions to transversions is typically around 2. In protein coding regions, this ratio is typically higher, often a little above 3. The higher ratio occurs because, especially when they occur in the third base of a codon, transversions are much more likely to change the encoded amino acid. A refinement to this analysis, in protein coding regions, is to examine the transition to transversion ratio separately for non-degenerate, two-fold degenerate, three-fold degenerate and four-fold degenerate sites.

http://genome.sph.umich.edu/wiki/SNP_Call_Set_Properties

---

Some useful papers:

Transition-Transversion Bias Is Not Universal: A Counter Example from Grasshopper Pseudogenes 

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.0030022

Estimation of the transition/transversion rate bias and species sampling

http://www.ncbi.nlm.nih.gov/pubmed/10093216

Mutational and fitness landscapes of an RNA virus revealed through population sequencing

http://www.nature.com/nature/journal/v505/n7485/full/nature12861.html

 

wget --random-wait

 --random-wait

Some web sites may perform log analysis to identify retrieval programs such as Wget by looking for statistically significant similarities in the time between requests. This option causes the time between requests to vary between 0.5 and 1.5 * wait seconds, where wait was specified using the --wait option, in order to mask Wget’s presence from such analysis.

A 2001 article in a publication devoted to development on a popular consumer platform provided code to perform this analysis on the fly.  Its author suggested blocking at the class C address level to ensure automated retrieval programs were blocked despite changing DHCP-supplied addresses.

The --random-wait option was inspired by this ill-advised recommendation to block many unrelated users from a web site due to the actions of one.

Install OpenVPN

Mainly refer to these web pages:
http://geek-kb.com/linux/install-and-configure-openvpn-centos-6-x/  (Tried this tutorial, but failed. Service failed.)
https://bugzilla.redhat.com/show_bug.cgi?id=966373   (In server.conf, plugin path was different for v2.3.1)

Try older version with "yum downgrade"!
http://www.sohailriaz.com/how-to-downgrade-rpm-package-using-yum/
http://blog.adityapatawari.com/2012/05/how-to-downgrade-or-reinstall-rpm.html




The following videos are based on openvpn-2.2.2.

VPN Setup using OpenVPN on CentOS 6.3 - part 1/2 

VPN Setup using OpenVPN on CentOS 6.3 - part 2/2