PLNT3140 INTRODUCTORY CYTOGENETICS

BIOINFORMATICS LAB 2023


Week of Sept. 11


1. Cloud-based Computing in Linux


Week of Nov. 20

2. Basic DNA sequence analysis

BEFORE this lab, login to Linux through Thinlinc, and do the following tutorials:

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.

VIDEO: BIRCH: Desktop Bioinformatics (short version, 17:01)
VIDEO (24:15) : Sequence File formats (24:15)


Working with sequences in BioLegato
 
Finding and retrieving complete eukaryotic genomes



Week of Nov. 27

3. Similarity searches and comparative genomics

BEFORE this lab, login to Linux through Thinlinc, and do the following tutorials:

Theory: Matrix Similarity Searches  VIDEO:VIDEO (35:45)
Tutorial: DXHOM  VIDEO:VIDEO (19:48)

Tutorial: Comparing genomes using dotplots


 
Tutorial: Comparing genomes using Mauve VIDEO:VIDEO (19:48)


Assignment - Comparison of Yeast Genomes

 

BIRCHGo to BIRCH home page

Send questions or comments on this web site to frist@cc.umanitoba.ca