From CSBLwiki

Contents 1 Pan-Genomic Space 1.1 Data 1.2 Results 1.2.1 Taxa-specific Pfam domains 1.2.2 MDS 1.3 R script sources

Pan-Genomic Space

Data

• Pan-Genome data version 0.1 Feb 2010
  • The frequency profile (1,137 genomes x 11,912 Pfam domains)
    • download: The FP(Frequency Profile) matrix

Results

Taxa-specific Pfam domains

• Hierarchical clustering of the FP profile
  

MDS

• Procedures

1. build a pairwise distance matrix (11,912 x 11,912) from the FP matrix (1,137 x 11,912) - euclidean distance
2. do MDS (multidimensional scaling) of the distance matrix
3. get coordinates from the first three dimension and plot them in a 3D-space

• MDS results

1. from Exact distance matrix:
   
2. from distance matrix cutting off at 99% of the maximum distance:
   
3. from distance matrix cutting off at 98% of the maximum distance:
   
4. from distance matrix cutting off at 97% of the maximum distance:
   

R script sources

• TBA