BLAST- searching for similarity

(Basic Local Alignment Search Tool)

Based on short parts of the query sequence program searches for similar sequences using „substitution matrix“, which defines the score of potential alignments. 

NCBI/BLAST  tutorial: 

Pairwise and Multiple comparisons of protein sequences - (multiple)alignment

Comparison is based on substitution matrix.

Pair global comparison: Needle (compare sequences in full length)

Pair local comparison: LALING (finds the most similar parts of two sequences)

Multiple alignments:

Multalin -a simple tool for comparison of two or more sequences

Clustal Omega - enables to display of phylogeny tree

Phylogenetic tree

Advanced phylogeny here.

3-D Structure

PDB (Protein Data Bank)

Specific databases:

Enzymes (Brenda), interactions (STRING)

Examples of typical tasks in exam test:

Ex1: Find two human DHRS7 sequences: DHRS7B (AAH09679.1) and DHRS7C (AAI47025.1) Run pair-wise alignment. How identical are these two proteins? Hint. Solution.

Ex2:  Find in Uniprot sequences of human NQO1 isoforms and align them. How many isofroms are there? Compare the alignment output to the description of each isoform, is it correct? Hint. Solution.

Ex3:Download the sequnce of "unknown protein" (here). Using domain prediction guess what is the function of the protein. Verify that by BLAST. What organism does it come from? Does it have any transmembrane helices?