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--- assignments:assignment3 [2015/10/02 10:04]
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+++ assignments:assignment3 [2015/10/02 12:05]
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 of distinguishing a particular class of proteins from a selection of
 examples sampled from the rest of the SCOP database
-using features derived from their sequence (note that a protein is an arbitrary length sequence over the alphabet of the 20 amino acids).
+using features derived from their sequence (a protein is a chain of amino acids, so as computer scientists, we can consider it as a sequence over the alphabet of the 20 amino acids).
-I chose to represent the proteins in
+I chose to represent the proteins in terms of their motif composition.  A sequence motif is a
-terms of their motif composition.  A sequence motif is a
 pattern of amino acids that is conserved in evolution.
 Motifs are usually associated with regions of the protein that are
@@ Line 41: / Line 40: @@
 so the data is very sparse.
 Therefore, only the non-zero elements of the data are represented.
-Each line in the file describes a single example and has the format:
+Each line in the file describes a single example.  Here's an example from the file:
 <code>

CS545 fall 2016