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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 (Bruce, 2000). 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 (Gavel and von Heijne, 1990; Emanuelsson et al., 1999)
(Bruce, 2000) Chloroplast transit peptides: structure, function and evolution. Trends Cell Biol.
(Emanuelsson et al., 1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci.
(Gavel and von Heijne, 1990) A conserved cleavage-site motif in chloroplast transit peptides. FEBS Lett.
(Richly and Leister, 2004) An improved prediction of chloroplast proteins reveals diversities and commonalities in the chloroplast proteomes of Arabidopsis and rice. Gene.