Pan-genome
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===MDS=== | ===MDS=== | ||
*Procedures | *Procedures | ||
| - | #build a pairwise distance matrix (11,912 x 11,912) from the FP matrix (1,137 x 11,912) - [ | + | #build a pairwise distance matrix (11,912 x 11,912) from the FP matrix (1,137 x 11,912) - [[w:Wikipedia:euclidean distance|Wikipedia:euclidean distance]] |
#do MDS (multidimensional scaling) of the distance matrix | #do MDS (multidimensional scaling) of the distance matrix | ||
#get coordinates from the first three dimension and plot them in a 3D-space | #get coordinates from the first three dimension and plot them in a 3D-space | ||
Revision as of 07:44, 12 March 2010
Contents |
Pan-Genomic Universe
Data
- Pan-Genome data version 0.1 Feb 2010
- Download the frequency profile (1,137 genomes x 11,912 pfam domains)
- download: The FP(Frequency Profile) matrix
Results
MDS
- Procedures
- build a pairwise distance matrix (11,912 x 11,912) from the FP matrix (1,137 x 11,912) - Wikipedia:euclidean distance
- do MDS (multidimensional scaling) of the distance matrix
- get coordinates from the first three dimension and plot them in a 3D-space
- Exact distance matrix
