Integrative Bioinformatics 7

[Index of classes ]

January 31 - Review of homework assignments - dynamic programming for sequence alignment and regular expressions:

1. Dynamic programming of Needleman-Wunch alignment algorithm.
2. Review of solutions to other alignment algorithms, note storing matrix indexes for traceback proceedures.
3. Visualization of scoring dynamic programming matrices.
4. Regular expression for tag delimitation in tabular formats.
5. Regular expression chalange.
6. Recommended new reading - upcomming chalanges/opportunities in sequence analysis:
   
   A Plan to Capture Human Diversity in 1000 Genomes [Science 25 January 2008]
   Scientists Synthesize a Genome From Scratch [ScienceNOW Daily News24 January 2008]
   

HOMEWORK
(note old solutions at http://ibl.mdanderson.org/~jalmeida/IB2008/)

Write you favorite implementation of a UCSC client in matlab and include with your m-files a archive html report describing its use, produced with cell programming + publish.