22 RNA Structure Function.ppt

10/31/05 RNA Structure & Function
1
D Dobbs ISU - BCB 444/544X: RNA Structure & Function
Announcements
Seminar (Mon Oct 31)
12:10 PM IG Faculty Seminar in 101 Ind Ed II
Plant Steroid Hormone Signal Transduction
Yanhai Yin, GDCB


BCB Link for Seminar Schedules (updated)
.edu/seminars/
2
D Dobbs ISU - BCB 444/544X: RNA Structure & Function
Announcements
BCB 544 Projects - Important Dates:

Nov 2 Wed noon - Project proposals due to David/Drena
Nov 4 Fri 10A - Approvals/responses to students
Dec 2 Fri noon - Written project reports due
Dec 5,7,8,9 class/lab - Oral Presentations (20')
(Dec 15 Thurs = Final Exam)
3
D Dobbs ISU - BCB 444/544X: RNA Structure & Function
RNA Structure & Function Prediction
Mon Review - promoter prediction
RNA structure & function
Wed RNA structure prediction
2' & 3' structure prediction
miRNA & target prediction
RNA function prediction?
4
D Dobbs ISU - BCB 444/544X: RNA Structure & Function
Reading Assignment (for Mon/Wed)
Mount Bioinformatics
Chp 8 Prediction of RNA Secondary Structure
pp. 327-355
Ck Errata: p/
Cates (Online) RNA Secondary Structure Prediction Module
/
5
D Dobbs ISU - BCB 444/544X: RNA Structure & Function
Review last lecture:Promoter Prediction
6
D Dobbs ISU - BCB 444/544X: RNA Structure & Function
Promoter Prediction
Overview of strategies
 What sequence signals can be used?
 What other types of information can be used?
Algorithms  a bit more about these
in later lectures
Promoter prediction software
3 major types
many, many programs!
7
D Dobbs ISU - BCB 444/544X: RNA Structure & Function
Promoter prediction: Eukaryotes vs prokaryotes
Promoter prediction is easier in microbial genomes
Why? Highly conserved
Simpler gene structures
More sequenced genomes!
(parative approaches)
Methods? Previously, again mostly HMM-based
Now: similarity-based. comparative methods
because so many genomes a