tr と rev を駆使すると簡単に書くことができます。
trで{A,T,G,C}をそれぞれ{T,A,C,G}に変換し、revで文字列を反転します。
#! /bin/bash
DNA="ATTGAATGATAGA"
echo ${DNA} | tr ATGC TACG | rev # TCTATCATTCAAT
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