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Revision as of 07:52, 12 March 2010 (view source) Igchoi (Talk | contribs) (→MDS) ← Older edit		Revision as of 07:53, 12 March 2010 (view source) Igchoi (Talk | contribs) (→Data) Newer edit →
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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 [http://pfam.sanger.ac.uk Pfam] domains)	+	**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]]	+	***<b>download: [[media:profile.csv|The FP(Frequency Profile) matrix]]</b>
	==Results==		==Results==

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Revision as of 07:53, 12 March 2010

Contents 1 Pan-Genomic Universe 1.1 Data 1.2 Results 1.2.1 MDS 1.3 R script sources

Pan-Genomic Universe

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

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