MeRecon: Carbon assimilation pathway of cassava tutorial
The carbon assimilation pathway of cassava (MeRecon) was reconstructed from the cassava genome version 4.1 (Phytozome version 7.0) with the reference pathway of six plant templates (Arabidopsis thaliana (Arabidopsis), Zea mays (maize), Oryza sativa (rice), Ricinus communis (castor bean), Solanum tuberosum (potato), and Brassica rapa (turnip)) by using the comparative genomics approach developed by Saithong T. et al., 2013, BMC Syst. Biol., 7:75. The conservation scores (CS) represent confidence of the identification relying on the consistency or the conservation of the identified gene in cassava among the six plant templates, and the match scores (MS) represent confidence of the identification based on the similarity of the two aligned sequences.
EC number |
found in MeRecon and CassavaCyc pathways |
EC number |
not found in MeRecon and CassavaCyc pathways |
EC number |
found only in CassavaCyc pathway |
EC number |
found only in MeRecon pathway |
| Arabidopsis thaliana (Arabidopsis) | |
| Zea mays (maize) | |
| Oryza sativa (rice) | |
| Ricinus communis (castor bean) | |
| Solanum tuberosum (potato) | |
| Brassica rapa (turnip) |
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reciprocal best hit (RBH) |
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not RBH, remain match best with the genes in the original query set |
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not RBH, remain match best with the genes in the genome that are not included in the original query set |