Starting with a tab separated file Use the reverse utility and sed to generate the reverse complement of a tabulated sequence file. cut -f2 file | rev | sed 'y/CGAT/GCTA/' You could also make the reverse complemented sequence in lower case using sed 'y/CGAT/gcta/' If you need the sequence name, paste it back. cut -f2 file | rev | sed 'y/CGAT/GCTA/' | paste file - Starting with a fasta Now starting with a fasta file. Avoid tabs and special characters in the sequence name. paste - - < file > tmp cut -f2 tmp | rev | sed 'y/CGAT/GCTA/' \ | paste tmp - | cut -f1,3 | tr '\t' '\n'