Award #0321460
Award #0604966
Award #0821966

Gene Families

Two methods were used to cluster proteins into families. The gene set used does not contain the genes classified as Transposable Elements (TEs).

TribeMCL clusters families by first running an all-versus-all BLAST search and parsing the output through matrices to generate the families. The ten largest families include:

Family ID	Num. Family Members	Name
1	861	Receptor-like protein kinase
2	840	Disease resistance-like protein
3	732	Unknown protein/Cytochrome P450
4	564	Leucine Rich Repeat family protein
5	335	Helicase-like protein
6	331	Cytochrome P450
7	325	NBS-LRR disease resistance protein
8	317	Pentatricopeptide repeat-containing protein
9	283	Pentatricopeptide repeat-containing protein
10	237	1-aminocyclopropane-1-carboxylate oxidase

The JCVI Paralogous Families pipeline clusters proteins into families based on domain composition. Domains are first identified by HMM search, and then by BLAST homology. The family members all contain the same domain architecture.

Family ID	Num. Family Members	Name
1	562	Unknown protein
2	304	Receptor-like protein kinase
3	247	Unknown protein
4	168	F-box/kelch-repeat protein
5	155	Helicase-like protein
6	150	Unknown protein
7	150	CCP
8	132	Unknown protein
9	128	Pentatricopeptide repeat-containing protein
10	121	Pentatricopeptide repeat-containing protein