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    • 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, Clustal Omega (calculates phylogeny tree), NCBI/COBALT

      Phylogenetic tree

       Clustal Omega (calculates phylogeny tree)

      Advanced phylogeny here.

    • 3-D Structure

      PDB (Protein Data Bank)

    • Specific databases:

      Enzymes (Brenda), interactions (STRING)

    • Examples:

    • 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?

    • Ex3_sequence identification Soubor
    • Lesson 4 - pdf Soubor
    • HW4: Protein comparison, 3D structure Úkol