# If you'd like to omit non-matching lines from the result; add ';d' to the end of the expression.
sed -E 's/;(?=(?:[^\[\]]*\[[^\[\]]*\])*[^\[\]]*$)
#;|\[|\]//gx;t' <<< "#first split:
gene1[position1:oldAA-newAA;position2:oldAA-newAA;position3:oldXX-newXX];gene2[position1:oldAA-newAA];gene3[v];gene4;gene5
#second split:
gene1[position1:oldAA-newAA;position2:oldAA-newAA;position3:oldXX-newXX]"
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for SED, please visit: https://www.gnu.org/software/sed/manual/html_node/The-_0022s_0022-Command.html