Your questions on Quiz #2 ?

Your questions on "first principle" approaches in Bioinformatics ?

ktups and wordsize?

Dotlet Demonstration

Go over Friday's Lab:
(also, if you still have problems to see wht this is about, check reading materials on HuskyCT)

Comparison of nucleotide sequence with introns vs. protein sequence it codes.

in Dotlet:

Using BLAST:

How many repeats do you identify when you compare the Methanopyrus sequence against itself?

Jalview is an excellent JAVA applet to inspect and edit multiple sequence alignments. It also allows inspection of protein space for the aligned sequences. This works surprisingly well.

Jalview Homepage,
Jalview as Java Web Start Application

Dataset (in custal format) for demo is here

Load all.txt into Jalview, colour options, mouse use,
PID tree,
Principle component analysis -> sequence space)
See the Jalview help pages for more information.

Reading assignments for Wednesday/Monday:

Glance through the wikipedia entry on the RNA world hypothesis

On WebCT:
Miller: A Production of a.a. under Possible primitive Earth Conditions
(optional: Joyce: The Rise and Fall of the RNA World)

For Friday read through chapter 5, pay attention to sections on clustalw and progressive alignment.

optional for next Monday:
Wächtershäuser: Evolution of the first metabolic cycles (on WebCT)

Next quiz is due next Monday -> here