Reading and Presenting Paper Assignment
Homework 1: Due Day: 11 AM, Monday, Sept 23. Send your programs by e-mail to
yanako@cs.widener.edu
Homework 1
Homework 2: Due Day: 11 AM, Monday, Oct 21. Send your programs by e-mail to
yanako@cs.widener.edu
Homework 2
Final Project Description and Information
Project
UPDATED Schedule:
- Start: Monday, Oct 28
- Initial Tables 1, 2 , 3, 4 from STEP 1 for Project Sequences are complete by Friday, Nov 15
- STEP 2 and Tables 1, 2, 3, 4 including BLAST results complete by Monday, Nov 18 (you can finish this
part during the class)
- STEP 3 complete by Monday, Nov 25
- Undate of Tables 1, 2, 3, 4 and sumamry of the project complete by Monday, Dec 2
- Submission date and presentations: Monday, Dec 2 and Wed, Dec 4
Additional Project Requirements and Tips:
While running BLASTX to identify sequences that are translated to
proteins, Use Standard(1) for Genetic Code and the following Databases:
- Non-redundant protein sequences (nr)
- UnitProtKB/Swiss-Prot
- If time permits, run for other databases as well
Output Suggestions:
You would need to output a huge amount of information. My suggestion
is to split the output into several files and output potential genes in
one file, pseudo-genes in the second file, compliment reverese potential
genes in the third file and compliment reverse pseudo-genes in the forth
file. In addition, it might be helpful to output the list of tuples that
only contains start, end and promoter score.
Here is an exampe of the Python File
Output
If you will decide to choose this option you don't need to use UNIX
redirection anymore. Run your program with python file_name.py
and check the output files.
Project Sequences - will be updated later
Project Submission Requirements
- Send your python source code to yanako@cs.widener.edu and Word file with the project results and summary to
ykortsarts@mail.widener.edu
More Help with Python
TESTING
Wed Nov 6 in class Testing
Project Sequences
Group 1: Last names starts with A - G
Sequence for Group 1
Group 2: Last names starts with H-Z
Sequence for Group 2