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Online Lectures on Bioinformatics

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Pairwise sequence comparison



Exercises

  1. Copy this sequence. Dotter is a tool to create dot-plots and to interactively view them.
    A description of dotter is given on this page.
    Follow the link on this page to download dotter.
    How does the dot-plot of the sequence above look like and why?
    (note: alternatively you may use the dotlet Java-Applet)
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    theory


    Here is an example of a protein sequence in Fasta-Format:
    >HBA_ALLMI      STANDARD;      PRT;   141 AA., 141 bases, E4DD63BA checksum.
    VLSMEDKSNVKAIWGKASGHLEEYGAEALERMFCAYPQTKIYFPHFDMSH
    NSAQIRAHGKKVFSALHEAVNHIDDLPGALCRLSELHAHSLRVDPVNFKF
    LAHCVLVVFAIHHPSALSPEIHASLDKFLCAVSAVLTSKYR
    
    The first line is the description line, which consists of three parts:
    • the first character '>' shows that the description line of a sequence follows
    • the string following the '>' and ending at the first space (' ') is the sequence id (HBA_ALLMI)
    • the rest of the description line may give additional information about the sequence.
    In this way several sequences may be represented by simple concatenation.

  2. Obtain the Swissprot entries of the yeast hexokinase A
    and yeast hexokinase B proteins (see above) and create one fasta-file
    which contains both sequences.
    (hint: Download the ReadSeq conversion tool)

  3. Align the yeast hexokinase A and yeast hexokinase B protein.
    (hint: use LALIGN which is found at Swissprot -> Proteomics tools)

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    theory


    Answers to the exercises.



    Comments are very welcome.
    luz@molgen.mpg.de