http://www.perlmonks.org?node_id=833648


in reply to simple perl script to trim a FASTA file

trim off x nucleotides from the beginning, and y nucleotides from the end
#!/usr/bin/perl while (<DATA>) { s/^(?!>)...(.*)..../$1/; # ^^^ ^^^^ # x=3 y=4 print; } __DATA__ >HWI-EAS158_40_3_1_46_535 GTGAATGCGTGATACAGGAATGTTCGTTGTGACCAT >HWI-EAS158_40_3_1_47_579 AAAGTGAATGCGTGATACAGGAATGTTCGTTGTGAC >HWI-EAS158_40_3_1_46_731 GTGTCATGCGTGATACAGGAATGTTCGTTGTGAAAA

For longer stretches you can also write .{N} (with N being the number of nucleotides to trim).