I have a file which has the following structure: >sequence1 ACGUCGGAUCUGACUGUAUCG >sequence2 ACGGUAUGUCUGUAUCUGUAUUCUG >sequence3 ACGUAUCUAUCGUAUCUGAUC ... I would like to extract only the first 15 characters of the lines that do NOT start with '>'. Can anyone help me? THANX!

I'm not a MAC guy, but this should give you a place to start. You might also have to use egrep: #!/bin/ksh rm -f datafile.tmp grep -v '^>' datafile > datafile.tmp while read line do nl=$(echo "$line"|cut -c1-15) echo "$nl" done < datafile.tmp

Or, instead of a shell script, you can use a simple perl command. perl -ne 'print $1,$/ if /^([A-Z]{15})/' filename