BioMed Research International / 2014 / Article / Psdc 1

Research Article

Mining Seasonal Marine Microbial Pattern with Greedy Heuristic Clustering and Symmetrical Nonnegative Matrix Factorization

Pseudocode 1

 Input: Sequence Set , Minimum Length with Polymers l,  Neighborhood
   Parameter , Clustering Threshold , MinClusterSize
Output: Clustering Result of Sequence Set
 {
 Seed = ;  // Initialize the Seed Sequence Set
 For ++   //  Traverse the Distance of the Input sequence and current Seed Set
      For ++ //  Compute Distance of and   (or Simmilary);
  If Meet Distance ,
   //  then Sequence Clustering Unit of , and output
    , ;
  Else
   //  with Neighbor Sequence Expanding Method, yield to   Neighbor Sequence  ( )
    , //  Expanding Current Seed Sequence Set
    ;
   End If
End For
 END For //  Travel all of Clustering Units, Subtract the Clustering Results the Parameter
    MinClusterSize
,
  Reassigned ( )  //  Recluster Sequence in Clustering Units base on the Nearest
  Neighbor Clustering Algorithm,  Assigned to the nearest cluster units , and   Meet
 End If
 }
Notes: denotes the th Seed Sequence in Sequence Set; Neighbor ( )  denotes
Neighbor Sequence  ( );   denotes Clustering Unit of .

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