Length differences for gene, transcript, and CDS

The lengths of gene, transcript, and CDS can be quite different in their lengths.

First we need to understand all of these three terms:

  • gene Of these three, gene is a big concept, which contains both transcript and CDS.

  • transcript A gene can have multiple forms of transcripts (a.k …

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Learn git and github

Learn git and github

  • What is git? Why we use it?
  • Common git commands
  • Remote git repository

install git and environmental setup

git setup

# tell git who you are
git config --global user.name "Zenith Nobel"
git config --global user.email "ZN@msu.edu"
git config --global color.ui true …
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Making maps in R

rMaps

I have been working on my population genetics project. One of the main thing is to plot the data in the context of the sampling locations. I have been searching all different kinds of solutions. One of the best for my application was to use the packages: maps, mapplots.

Below …

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Compile Bio++ and install egglib on Ubuntu 14.04 LTS

I didn't find it difficult to install or compile the egglib module on Linux, when I first come to use egglib in python. However, things changed my mind when I was trying to use the internal function Align.polymorphismBPP(), which is a function that depends on the Bio++ library supoort …

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Good and useful bioinfomatics tools

Here below are the list of softwares I found to be very handy for applied bioinformatics. Most of the tools I listed here are open-source program.

  • PRANK - Codon sequence alignment
  • MAFFT - Multiple sequence alignment, similar performance to MUSCLE
  • egglib - powerful tools for population genetics and genomics data analysis
  • Roary - tool …
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Population genetics simulation in Python

A python script writen in OOP style to simulate population genetic dfrit and spontaneous mutation. Microsatellite markers were used as a surrogate to calculate genetic diversity across time/generations.

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