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
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