Pan-genome
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==Data== | ==Data== | ||
*<b>Pan-Genome data version 0.1 Feb 2010</b> | *<b>Pan-Genome data version 0.1 Feb 2010</b> | ||
| - | *Download the frequency profile (1,137 genomes x 11,912 pfam domains) | + | *Download the frequency profile (1,137 genomes x 11,912 [http://pfam.sanger.ac.uk Pfam] domains) |
**download: [[media:profile.csv|The FP(Frequency Profile) matrix]] | **download: [[media:profile.csv|The FP(Frequency Profile) matrix]] | ||
Revision as of 07:46, 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) - 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
