PLNT2530 Plant Biotechnology


Hint for Success: About half of doing well in these tutorials and assignments boils down to "Can you follow directions?". Therefore, the strategy should always be
  • read carefully
  • understand
  • do

1. Introduction to Linux

A. Tutorial: Connecting to Linux from Windows
B. Tutorial: Setting up your Linux account
C. Network-centric computing and Unix
D. Finding information
E. Tutorial: The GNOME Desktop

Assignment 1

2. Searching for and retrieving sequences from NCBI

BEFORE this lab, login to Linux through Thinlinc, and go through Unix Tutorial for Beginners (Duke University), through Tutorial Four.

Note:  Be sure to pay attention to the first section on "Typographical Conventions", regarding the command prompt. The prompt is what the shell prints each time to tell you that the last command has completed, and that it is waiting for you to type another command. The Duke tutorial uses the % character as the command prompt. When we ran the newuser script in the previous session, the command prompt was changed to include the name of the login host and the path to the current working directory. Therefore, your prompt will look something like


In the Duke tutorial, the command that you type is shown to the right of the prompt. You don't type the prompt itself.

This tutorial will use as an example sequences for cloning vectors used in the lab component.

A. GenBank file format
B. Tutorial: Finding and retrieving sequences from NCBI

Assignment 2


3. Simulated cloning

UGENE podcast, episode #2: Working with a sequence: basic operations part 1
UGENE podcast #12: Searching restriction enzymes cut sites with UGENE

Tutorial Introduction to Ugene

Assignment 3

4. In-silico cloning of genes by PCR

Assignment 4

BIRCHGo to BIRCH home page

Send questions or comments on this web site to