| Topic |
Date |
Remarks |
| Background and Intro to Python |
09/05/12 |
Basic molecular biology Intro to Python |
| Lists, input and output | 09/10/12 |
See previous slides |
| Lists, input and output | 09/12/12 |
See slides from first lecture HW 1 |
| For loop | 09/17/12 |
See slides from first lecture HW 2 |
| More loops |
09/19/12 |
HW 3 |
| More loops |
09/24/12 |
HW 4 |
| More loops |
09/26/12 |
HW 5 |
| DNA complements |
10/01/12 |
HW 6 |
| Transcription and translation |
10/03/12 |
HW 7 Codon to amino acid map |
| Translation | 10/08/12 |
HW 8 |
| Translation and review | 10/10/12 |
|
| First exam | 10/15/12 |
|
| Sequence alignment |
10/17/12 |
Sequence alignment HW 9 |
| Exam solution | 10/22/12 |
HW 10 |
| Conserved columns | 10/24/12 |
Hands-on bioinformatics
exercise HW 11 |
| NJIT closed due to hurricane Sandy |
10/29/12 | |
| NJIT closed due to hurricane Sandy |
10/31/12 | |
| Conserved columns |
11/05/12 | HW 11 reassigned |
| Conserved columns |
11/07/12 | HW 12 |
| Conserved columns, data formats (FASTA and PHYLIP), and while loops |
11/12/12 |
FASTA and PHYLIP formats HW 13 |
| Split function, data formats, and dictionaries | 11/14/12 | HW 14 |
| 11/19/12 |
HW 15 Practice problem |
|
| NJIT classes follow Friday schedule | 11/21/12 | |
| 11/26/12 |
HW 16 |
|
| 11/28/12 | ||
| Second exam | 12/03/12 | |
| Second exam solution | 12/05/12 | HW 17 |
| Extra credit assignment | 12/10/12 | Extra credit assignment BLOSUM 62 matrix alignments2.fasta |
| Review | 12/12/12 |
Substring alignment problem Genome assembly problem |
| Final exam | 12/20/12 | FMH 310, 8:30 to 11am |