Exercises Pairwise alignment Homology search BLAST Multiple alignment

Exercises • • Pairwise alignment Homology search (BLAST) Multiple alignment (CLUSTAL W) Profile Search – Pfam – Prosite • Iterative Profile Search: – PSI-BLAST – SAM

Exercises Dotlet

Global alignment Exercises • EMBOSS 1) Align sequences from dataset 1 1) Compare with the multiple alignment 2) Study the effect of the gap parameters 2) Align dataset 2 3) Align dataset 3 1) Compare the score between dataset 2 and 3 2) Can scores be compared? 3) Is it easy to determine relevance of alignment by visual inspection

Exercises Clustal. W

Exercises Clustal. W

Exercises Pairwise Alignment

Exercises global Pairwise Alignment

Local Exercises • 1) local alignment of dataset 1 – Compare with global alignment • 2) local alignment of dataset 2 – Compare with global alignment – Verify whether you find the right alignment by comparing the result to the multiple alignment – Test the effect of using PAM 25 and PAM 120 with identical parameter settings of the gap • 3) local alignment of dataset 3

Exercises Pairwise Alignment

Exercises Pairwise alignment Dataset 2

Exercises

Exercises Fast. A

NCBI Exercises Literature database Sequence database Blast tool

Exercises Homology Search

Exercises Homology Search Blast DNA sequence against non redundant database Blast protein sequence against non redundant database Blast translated DNA sequence against non redundant database

Exercises Homology Search

Exercises Homology Search

Exercises Homology Search

Exercises Homology Search

Exercises Homology Search

Exercises Homology Search

Exercises

Exercises

Exercises Add to clipboard

Exercises Select from protein DB

Exercises Select sequences

Exercises

Exercises Clustal. W

Exercises Clustal. W

Exercises Clustal. W

Exercises Pairwise alignment Dataset 2

Exercises Multiple Alignment Multiple alignment: standard gap cost Ligands Cu center Ligands hemes

Exercises

Exercises Multiple alignment: large gap cost Multiple Alignment

Exercises Tree based on subselection Phylogenetic Tree

Exercises http: //genome. cs. mtu. edu/align. html Pairwise Alignment

Exercises Pairwise Alignment

Exercises Pairwise Alignment Compare with multiple alignments later local