A 10-week course designed for Whitehead Scientists

Monday at 10am in the Auditorium at 9CC

Instructors: Fran Lewitter, Head of Biocomputing; George Bell, Biocomputing Applications Specialist; Robert Latek, Biocomputing Applications Specialist, Bingbing Yuan, Biocomputing Applications Programmer.

Purpose: This course is intended to provide a basic understanding of the algorithms, methods and limitations of Bioinformatics tools. In addition, basic programming tools will be taught and applied in the field of genomics.

Format: A lecture lasting about 1 hour and 15 minutes followed by a demo of relevant tools available at Whitehead lasting for about fifteen minutes . Homework will be given after each lecture.


Supplemental Texts:

Syllabus: Homework Course Evaluation Form
Chapters in Mount
January 7 Sequence Analysis I. Pairwise alignments, database searching including BLAST To print, Slide show (FL) 1, 2, 3
January 14 Sequence Analysis II. Database searching (continued), Pattern searching To print, Slide show (FL) 7
January 21 No Class - Martin Luther King Holiday
January 28 Sequence Analysis III. Hidden Markov models, gene finding algorithms To print, Slide show (FL) 8
February 4 Computational Methods I. Genomic Resources and Unix   To print, Slide show (GB) Gibas 3,4,5
February 11 Computational Methods II. Sequence analysis with Perl.   To print, Slide show (GB) Baxevanis 17, Gibas 12
February 18 No Class - President's Birthday  
February 25 Computational Methods III. Sequence analysis with Perl and BioPerl   To print, Slide show (GB) Baxevanis 17, Gibas 12
March 4 Proteins I. Multiple sequence alignments, phylogenetic trees To print, Slide show (RL) 4, 6
March 11 Proteins II. Profile searches of databases, revealing protein motifs To print, Slide show (RL) 9
March 18 Proteins III.Structural Genomics - structural comparisons and predictions To print, Slide show (RL)  
March 25 Microarrays: designing chips, clustering methods To print, Slide show(FL)