Association algorithm to mine the rules that govern enzyme definition and to classify protein sequences.
BACKGROUND
The number of sequences compiled in many genome projects is growing exponentially, but most of them have not been characterized experimentally. An automatic annotation scheme must be in an urgent need to reduce the gap between the amount of new sequences produced and reliable functional annotation. This work proposes rules for automatically classifying the fungus genes. The approach involves elucidating the enzyme classifying rule that is hidden in UniProt protein knowledgebase and then applying it for classification. The association algorithm, Apriori, is utilized to mine the relationship between the enzyme class and significant InterPro entries. The candidate rules are evaluated for their classificatory capacity.


RESULTS
There were five datasets collected from the Swiss-Prot for establishing the annotation rules. These were treated as the training sets. The TrEMBL entries were treated as the testing set. A correct enzyme classification rate of 70% was obtained for the prokaryote datasets and a similar rate of about 80% was obtained for the eukaryote datasets. The fungus training dataset which lacks an enzyme class description was also used to evaluate the fungus candidate rules. A total of 88 out of 5085 test entries were matched with the fungus rule set. These were otherwise poorly annotated using their functional descriptions.


CONCLUSIONS
The feasibility of using the method presented here to classify enzyme classes based on the enzyme domain rules is evident. The rules may be also employed by the protein annotators in manual annotation or implemented in an automatic annotation flowchart.
Chiu
Shih-Hau
SH
Bioresource Collection and Research Center, Food Industry Research and Development Institute, HsinChu, Taiwan. shc@firdi.org.tw
Chen
Chien-Chi
CC
Yuan
Gwo-Fang
GF
Lin
Thy-Hou
TH
D000465:Algorithms; D003628:Database Management Systems; D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry* / Q000145:classification*; D005656:Fungal Proteins / Q000737:chemistry* / Q000145:classification*; D016247:Information Storage and Retrieval / Q000379:methods; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*
D004798:Enzymes; D005656:Fungal Proteins