Been whacking at this one for a while, and it eludes me.

((T ACC) (I ATT) (T ACT) (P CCA) (E GAA) (T ACT) (S TCC) (R CGT) (P CCA) 
(I ATC) ;0-9
(T ACT) (M ATG) (D GAT) (H CAC) (L CTG) (E GAG) (K AAA) (N AAC) (E GAA) 
;1210-1218)

remove only single leading paren (
remove only trailing single paren )
leave all others

remove ;xxx-yyy at the end of each line (unix line) where xxx is a 
number and yyy is a number

so that the result looks like:

(T ACC) (I ATT) (T ACT) (P CCA) (E GAA) (T ACT) (S TCC) (R CGT) (P CCA) 
(I ATC) (T ACT) (M ATG) (D GAT) (H CAC) (L CTG) (E GAG) (K AAA) (N AAC) 
(E GAA)

You will advance the state of genomic science !!!

(yuck ... I hate RE ...)

Rick


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