BLAST and the commandline

Assignments for Wednesday

Assignments for Wednesday (Friday by the latest)

Read through the first three and the last items on the Dotlet help pages.
Dotlet is a program that "aligns" DNA with DNA, or amino acid with amino acid, or 3 frame translations of DNA with aa sequneces.
It calculates and analyzes the alignment scores (without introducing gaps) for all possible windows in the two sequences.

Discuss Takehome exam #3

ELSE

analysis for pairwise genome comparison is here (discuss %identity, alignment lengthd, #of identical aa)
discuss blastall, example
blastall -i ACN -d CCI3 -o blast.out -p blastp -e 0.000001 -m 8 -a 2
example of what one could do with this:
- (perl script to extract top scoring hits is here)
- (perl script to replace gi number with position on the genome is here)
- (perscript to make gnuplot is here, output for two Thermotoga genomes is here, several genome plots from Frankia with differnet E-value cut-offs are here)

If time, discuss ppt slides from class 4.