Autumn 2005

October 4

Organizational Meeting

October 11

Presentation by Kasia
Identifying ncRNAs in AT-rich genomes

Background Paper:

Klein, R.; Misulovin, Z. & Eddy, S. Noncoding RNA genes identified in AT-rich hyperthermophiles Proceedings of the National Academy of Sciences in the United States, 2002, 99, 7542-7547
ABSTRACT:
Noncoding RNA (ncRNA) genes that produce functional RNAs instead of encoding proteins seem to be somewhat more prevalent than previously thought. However, estimating their number and importance is difficult because systematic identification of ncRNA genes remains challenging. Here, we exploit a strong, surprising DNA composition bias in genomes of some hyperthermophilic organisms: simply screening for GC-rich regions in the AT-rich Methanococcus jannaschii and Pyrococcus furiosus genomes efficiently detects both known and new RNA genes with a high degree of secondary structure. A separate screen based on comparative analysis also successfully identifies noncoding RNA genes in P. furiosus. Nine of the 30 new candidate genes predicted by these screens have been verified to produce discrete, apparently noncoding transcripts with sizes ranging from 97 to 277 nucleotides.

October 18

Presentation by Amol

Background Paper:

ABSTRACT:

October 25

Presentation by Jonathan

Background Paper:

ABSTRACT:

November 1

November 8

November 15

November 22

November 29

December 6

Computer Science & Engineering
University of Washington
Box 352350
Seattle, WA 98195-2350
(206) 543-1695 voice, (206) 543-2969 FAX
[comments to Katarzyna Wilamowska]