Course Schedule

DATE	TOPIC	Sub-Topics	Instr.
Jan 11	Welcome, sylabus	Intro to Bioinformatics	Mike
Jan 13	Learning about iNquiry	Exercise 1	Mike

Jan 18	Bioinformatics tools	Bioinformatics: small tools, complex tools, one goal	Mike
Jan 20	Unix	The standard OS for science	Mitch

Jan 25	Perl	A computer language for sequence analysis	Mitch
Jan 27	More Perl (& homework assigned)	Making a Perl script	Mitch

Feb 01	BioPERL	Modules & shortcuts for Perl applications	Mitch
Feb 03	EMBOSS & iNquiry	Using bioinformatics applications	Mike

Feb 18	Alignments	Pairwise sequence alignments: scoring matrices - Slide Show, Matrix Usage	Mike
Feb 10	Alignments	Pairwise sequence alignments: dynamic programming for global and local alignments, intro to BLAST - Slide Show	Mike

Feb 15	Tool: BLAST	BLAST: Using, interpretting, specialized features, similar tools - Slide Show	Mike
Feb 17	Tool: BLAST	Advanced BLAST: PSI-Blast, PHI-Blast - Slide Show	Mike

Feb 22	Homework Presentations
Feb 24	Homework presentations		Mike

Mar 01	Multiple Sequence Alignments	ClustalW, HMM's - Slide Show	Mike
Mar 03	Perl for parsing data	Data format structure, finding and parsing data	Mitch

Mar 08	class cancelled
Mar 10	Multiple Sequence Alignments	Advanced MSA: issues, applications	Mike

Mar 15	SPRING BREAK
Mar 17	SPRING BREAK

Mar 22	Gene Prediction	Theory & application - Slide Show	Mike
Mar 24	Gene Prediction - Mike's Slide Show	Tool presentation: gene finding tools - Eric's Slide Show	Mike, James Lee

Mar 29	Genome analysis - Mike's Slide Show	Tool presentation: Sequence alignments - multiple, consensus - Lyla's Slide Show	Mike, Lyla Lipscomb
Mar 31	Genome analysis - Mike's Slide Show	Tool presentation: Sequence alignments - dot plots, global, local - Pahresah's Slide Show	Mike, Pahresah Roomiany

Apr 05	Genome analysis - Mike's Slide Show	Tool presentation: Nucleotide sequence composition, codon usage, translation, mutation, profiles, 2d structure	Mike, Erin Olson
Apr 07	Genome analysis - Mike's Slide Show	Tool presentation: Nucleotide sequence transcription, restriction, primers, repeats, motifs, cpg islands Tejas' Slide Show	Mike, Tejaswita Karve

Apr 12	Protein analysis & proteomics - Mike's Slide Show	Tool presentation: Protein sequence composition, profiles, mutation, MOTIFS	Mike, Zhen Li
Apr 14	Protein analysis & proteomics - Mike's Slide Show	Tool presentation: Protein sequence 2d structure, 3d structure	Mike, Amy Runck

Apr 19	Protein analysis & proteomics	Tool presentation: Profile HMM for protein searches	Mike, Deborah Johnson
Apr 21	Gene Expression Analysis	Tool presentation: Gene Expression Analysis	Mike, Quinn Shurtliff

Apr 26	Phylogenetics	Tool presentation: Likelihood, parsimony approaches	Mike, Kayce Bell
Apr 28	Phylogenetics	Tool presentation: Distance approaches	Mike, Kurino Ashizawa

May 01	Phylogenetics	Tool presentation: MrBayes	Mike, Eric Waltari
May 03	TBA