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

[download]

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

In reply to Re: simple perl script to trim a FASTA file by almut
in thread simple perl script to trim a FASTA file by RabidMortal

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