Methods of producing modified nucleic acid sequences for eliminating adverse splicing events

A method for generating a modified nucleic acid sequence comprising: (a) providing a target nucleic acid sequence (Seqtarget) comprising an open reading frame, wherein Seqtarget has a length (Ntarget), (b) defining an organism-dependent splicing model comprising: compiling a listing of sequence contexts (Seqcon) comprising one or more intron/exon boundary sequences having a length (Ncon), and putative splice donor (SD) sequence contexts (SeqconSD) and putative splice acceptor (SA) sequence contexts (SeqconSA), to obtain patterns (P) of length (Ncon) from Seqcon, calculating a predictive splice score for each pattern P for determining whether such pattern P indicates the presence of a putative SD sequence motif or SA sequence motif, (c) providing a splice site identifying algorithm (Ai) to define a third quality function capable of computing for each nucleic acid sequence of length (N) a predictive splice score, for the presence of a putative splice sequence motif; (d) applying a splice site modifying algorithm (AM) iteratively generating the modified nucleic acid sequence with silent splice site mutations.