CIS700 class notes by Junwen Wang

12Jan06

General advice for reading paper

•     understand the basic idea
•     the purpose of the research
•     how they do it?
•     how they perform the experiments

Alternative splicing

•     Is first exon more conserved?
•     Does the position of the enhancer or silencers matter? are they position specific?
•     how is alternative splicing related to tissue specificity?
•     CpG island and splicing
•     in burge paper, why they claim 10% coverage?
•     know the structure of splicesome and how it interacts with RNA

Motif finding algorithm

•     in weeder, they allow 1 mismatch for 6-mer, 2 for 8-mer and 4 for 12-mer
•     how to improve the representation of motifs

Graph alignment

•     graph matching
•     graph alignment, signaling networks

Answer for first exon conservation

based on human mouse conservation on all refSeq genes, (hg16 and mm5), I calculated the average conservation human-mouse genes. As shown in table below, first and last exon are more conserved than the exons in the middle.