#!/usr/bin/perl -w my @contigfile = (">37","ABC","DEF","GHI","JKL","MNO","PQR","STU","VWX","YZ",">38"); my $element1 = 0; my $element2 = 0; # print @contigfile; # print substr($contigfile[$element1],0,1); # print $contigfile[$element1]; while ($contigfile[$element1]){ if (substr($contigfile[$element1], 0, 1) eq '>'){ do { ++$element2; } until (substr($contigfile[$element2], 0, 1) eq '>'); $new = join('',@contigfile[($element1 + 1)..($element2 - 1)]); splice @contigfile, $element1, $element2, "$new"; ++$element1; $element2 = $element1; } } print @contigfile; exit;