( ( ( Current programs ) ( for ( gene assignment ) ) ) ( ( are ( ( based largely ) ( on ( characteristics ( of ( ( ( protein sequences ) ( such ( as ( ( ( ( ( ( start ( and ( stop codons ) ) ) , ) ( ribosome ( binding site ) ) ) , ) and ) ( amino ( acid ( coding biases ) ) ) ) ) ) ) ( which ( ( are not ) ( applicable ( to ( RNA ( coding regions ) ) ) ) ) ) ) ) ) ) ) ) . ) )
(ROOT (S (NP (NP (JJ Current) (NNS programs)) (PP (IN for) (NP (NN gene) (NN assignment)))) (VP (VBP are) (VP (VBN based) (ADVP (RB largely)) (PP (IN on) (NP (NP (NNS characteristics)) (PP (IN of) (NP (NP (NN protein) (NNS sequences)) (PP (JJ such) (IN as) (NP (NP (NN start) (CC and) (VB stop) (NNS codons)) (, ,) (NP (NN ribosome) (VBG binding) (NN site)) (, ,) (CC and) (NP (JJ amino) (JJ acid) (VBG coding) (NNS biases)))) (SBAR (WHNP (WDT which)) (S (VP (VBP are) (RB not) (ADJP (JJ applicable) (PP (TO to) (NP (NNP RNA) (VBG coding) (NNS regions))))))))))))) (. .)))
Current programs for gene assignment are based largely on characteristics of protein sequences such as start and stop codons, ribosome binding site, and amino acid coding biases which are not applicable to RNA coding regions.
(ROOT (S (SBAR (WHADVP (WRB When)) (S (NP (NP (DT a) (NN chain)) (PP (IN of) (NP (JJ amino) (NNS acids)))) (VP (VBZ reaches) (NP (DT a) (NN stop) (NN codon))))) (, ,) (VP (VBN released) (PP (IN from) (NP (DT the) (NN ribosome)))) (. .)))