Pan-genome
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- | =Pan-Genomic | + | =Pan-Genomic Space= |
==Data== | ==Data== | ||
- | *Pan-Genome data version 0.1 Feb 2010 | + | *<b>[[w:pangenome|Pan-Genome]] data version 0.1 Feb 2010</b> |
+ | **The frequency profile (1,137 genomes x 11,912 [http://pfam.sanger.ac.uk Pfam] domains) | ||
+ | ***<b>download: [[media:profile.csv|The FP(Frequency Profile) matrix]]</b> | ||
+ | |||
==Results== | ==Results== | ||
+ | ===Taxa-specific Pfam domains=== | ||
+ | *Hierarchical clustering of the FP profile<br>[[image:taxaSdom.png|800px]] | ||
+ | |||
+ | ===MDS=== | ||
+ | *Procedures | ||
+ | #build a pairwise distance matrix (11,912 x 11,912) from the FP matrix (1,137 x 11,912) - [[w:Euclidean distance|euclidean distance]] | ||
+ | #do MDS ([[w:multidimensional scaling|multidimensional scaling]]) of the distance matrix | ||
+ | #get coordinates from the first three dimension and plot them in a 3D-space | ||
+ | *MDS results | ||
+ | #from Exact distance matrix:<br>[[image:mds1.png]] | ||
+ | #from distance matrix cutting off at 99% of the maximum distance:<br>[[image:mds99.png]] | ||
+ | #from distance matrix cutting off at 98% of the maximum distance:<br>[[image:mds98.png]] | ||
+ | #from distance matrix cutting off at 97% of the maximum distance:<br>[[image:mds97.png]] | ||
+ | |||
==R script sources== | ==R script sources== | ||
+ | *TBA |
Latest revision as of 06:49, 13 March 2010
Contents |
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
- The frequency profile (1,137 genomes x 11,912 Pfam domains)
Results
Taxa-specific Pfam domains
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
- MDS results
- from Exact distance matrix:
- from distance matrix cutting off at 99% of the maximum distance:
- from distance matrix cutting off at 98% of the maximum distance:
- from distance matrix cutting off at 97% of the maximum distance:
R script sources
- TBA