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)
   
   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)
   
   
   theory
   
   Answers to the exercises.
   
   

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