( ( ( The convention ) ( we use ) ) ( ( is ( ( UPPERCASE LETTERS ) ( ( ( ( represent ( amino acids ) ) ( -LRB- ( ( e.g. ( , ( VALQRK ... ) ) ) -RRB- ) ) ) and ) ( lowercase ( letters ( represent ( environments ( -LRB- ( ( ( ( ( letters a. ) . ) . ) r ) -RRB- ) ) ) ) ) ) ) ) ) . ) )
(ROOT (S (NP (NP (DT The) (NN convention)) (SBAR (S (NP (PRP we)) (VP (VBP use))))) (VP (VBZ is) (S (NP (NNP UPPERCASE) (NNP LETTERS)) (VP (VP (VB represent) (NP (JJ amino) (NNS acids)) (PRN (-LRB- -LRB-) (FRAG (INTJ (UH e.g.)) (, ,) (NP (NNP VALQRK)) (: ...)) (-RRB- -RRB-))) (CC and) (VP (VB lowercase) (S (NP (NNS letters)) (VP (VB represent) (NP (NP (NNS environments)) (PRN (-LRB- -LRB-) (X (X (SBARQ (WHNP (WHNP (JJ letters)) (ADJP (JJ a.))) (. .)) (. .)) (NP (SYM r))) (-RRB- -RRB-))))))))) (. .)))
The convention we use is UPPERCASE LETTERS represent amino acids (e.g., VALQRK...) and lowercase letters represent environments (letters a...r).
(ROOT (S (SBAR (WHADVP (WRB When)) (S (VP (VBD represented) (PP (IN by) (NP (DT a) (JJ single) (NN letter)))))) (, ,) (NP (JJ dominant) (NNS alleles)) (VP (VBP are) (VP (VBN represented) (PP (IN by) (NP (JJ uppercase) (NNS letters))))) (. .)))