Bioinformatics Schedule

Date	Topic	Reading	Assigned	Due
Jan 12	Bioinformatics overview; Syllabus; Unix, Perl and Editors Unix Tutorial Getting Perl on Windows (conversion issues) Perl Documentation All things Perl and Bioperl Editors: SubEthaEdit and Text Wrangler for Mac OS X; WordPad or SciTE for Windows BOOK PAGES: LeBlanc and Dyer Textbook web page LD Author's textbook web page St. Clair and Visick web page Errata for St. Clair and Visick	SV Ch 1 SV Ch 2 through p. 29	HW 1
14	NO CLASS; Meet with partner to discuss reading and do HW assignment
19	String Manipulation Calculations Class notes for strings and numbers GC-content	LD Ch 1-3 and 5
21	Control Structures New link to GC-skew page (also updated in HW 2 pdf file)	LD Ch 6	HW 2	HW 1
26	Catch up day; Control structures, continued
28	Subroutines Sequence comparison, part 1: dot plots	LD Ch 7 SV pp. 29-52	HW 3	HW 2 Discussion
Feb 2	Reading from files	LD Ch 8
4	Arrays	LD Ch 9	HW 4	HW 3
9	Arrays, continued
11	Arrays, continued Sequence comparison, part 2 (Helping Romina solve a problem)		HW 5	HW 4
16	Approximate gene alignments (BLAST, BLAST2, ClustalW) EMBOSS (use dottup for dot plots, needle for global alignment, water for local alignment)	SV pp. 53-81
18	Global and local gene alignments, cont. (Needleman-Wunsch, Smith-Waterman)	SV Ch 3	MIDTERM	HW 5
23	Protein alignments Amino acid properties Short and Long BLAST tutorials Substitution matrices: PAM30, BLOSUM62 [and how it was created], and a comparison	SV Ch 4
25	More on orthologs, paralogs, and homologs Hash tables Command-line bl2seq	LD Ch 10 SV Ch 4		MIDTERM (due Fri midnight)
	SPRING BREAK
March 9	Web forms, CGI scripts and Project 1 Example: GC skew		Project 1
11	RNA structure prediction Regular expressions, part 1	SV Ch 7 LD Ch 4
16	Protein structure prediction Regular expressions, part 2	SV Ch 7 LD Ch 12
18	Gene finding, part 1 ORF Finders at NCBI, SMS and EMBOSS IUPAC Codes	SV Ch 6
23	Gene finding, part 2 PWM files TESTCODE online tool and paper LuxI submitted and optimized Codon usage table Codon usage analysis tool
25	Genome rearrangement
30	Project work day
April 1	Project presentations			Project 1
6	EASTER BREAK
8	Genome rearrangement, continued Genome annotation paper, wiki 08, wiki 09	SV Ch 5	Project 2
13	Phylogenetic tree reconstruction: Molecular evolution models	SV Ch 8
15	Phylogenetic tree reconstruction
20	Microarray data analysis	SV Ch 9
22	Microarray data analysis
27	Project work day (IN CLASS), Final preparation
29	Project presentation; Course evaluations			Project 2
May 4	Class party; Final exam goes out
May 10	Final exams due at NOON (Seniors)
May 12	Final exams due at NOON (non-seniors)