Chloroplast protein sequence detection software tools
Large-scale detection of chloroplast proteins can be attempted only in silico. However, computational prediction of cTPs is hampered by the fact that N-terminal transit peptides are also used for targeting proteins to the mitochondrion (by mitochondrial transit peptides, mTPs) or to the secretory pathway (by secretory pathway signal peptides, SPs). In addition, cTPs are highly divergent in length, composition and organization. Furthermore, their secondary structure is not well characterized, and the degree of sequence conservation observed around the site cleaved by the stromal processing peptidase is quite low.
A web based tool for prediction of chloroplast proteins. ChloroPred takes an amino acid sequence as input and predicts chloroplast proteins with Support Vector Machine (SVM) and weka-SMO classifier. These methods have been trained and tested using five-fold cross-validation on a dataset of 712 proteins.
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