Exercise 6

EU name: EXE006

If you understand the amino acids, you understand everything, including difficult sequence alignments.
Hydrophobicity is the most important factor when dealing with amino acids, but when the hydrophobicity doesn't give you the answer, size, charge, and secondary structure preference will also contribute.

Figure 8. An attempt to sort all amino acids such that hydrophobicity, size, charge, secondary structure preference, sulphur presence, alcoholicity, aromaticity, etc., all are incorporated will always fail (sorry for the typos in the residue names).

The picture shown above comes close, but far from close enough to use without your brain switched on...

For each of the following examples, work out which is the better alignment: the right or the left. To do this well, you can choose between cheating and understanding the amino acids. 

    CPISRTWASIFRCW    CPISRTWASIFRCW
    CPISRT---LFRCW    CPISRTL---FRCW


    CPISRTRASEFRCW    CPISRTRASEFRCW
    CPISRTK---FRCW    CPISRT---KFRCW


    CPISRTIASNFRCW    CPISRTIASNFRCW
    CPISRTH---FRCW    CPISRT---HFRCW


    CPISRTEASDFRCW    CPISRTEASDFRCW
    CPISRT---NFRCW    CPISRTN---FRCW


    CPISRTSASIFRCW    CPISRTSASIFRCW
    CPISRT---TFRCW    CPISRTT---FRCW


    CPISRTGASIFRCW    CPISRTGASIFRCW
    CPISRTA---FRCW    CPISRT---AFRCW


    CPISRTEASNFRCW    CPISRTEASNFRCW
    CPISRTQ---FRCW    CPISRT---QFRCW


    CPISRTFASTFRCW    CPISRTFASTFRCW
    CPISRT---YFRCW    CPISRTY---FRCW

Question 10: Write down for each of these eight pairs of alignments which is the better one, left or right. Keep in mind that the first four are simple, but after that they rapidly become more difficult.

Answer

NOTE