PLNT2530 Plant Biotechnology

BIOINFORMATICS 2024

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 (in this order)"
  1. read carefully
  2. understand
  3. do



1. Introduction to Linux

Goals:

A. VIDEO: What most biologists probably don't know about computers (57:39)

B. Tutorial: Connecting to Linux

C. Tutorial: Setting up your Linux account

VIDEO:Watch the video before doing  this tutorial (9:03)

D. Finding information

F. Tutorial: The Xfce 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

{mars:/home/plants/frist}

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

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

VIDEO (24:15) : Sequence File formats (24:15)

Tutorial: User Settings


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 frist@cc.umanitoba.ca