Please read this documentation to help you learn: perlfunc, perlretut, perlreftut, perlre. 
#!/usr/bin/perl

use strict;
use warnings;

my %sequences;

# read the input files, passing in a filename and
# a reference to the sequences hash
read_file("file1", \%sequences);
read_file("file2", \%sequences);

# write the output file, passing in a filename and
# a reference to the sequences hash
write_file("file3", \%sequences);

sub read_file
{
    my $filename = shift;
    my $seqref = shift;

    open SEQFILE, "<$filename" or die "can't open $filename: $!";

    # use greater-than for record separator
    # see perldoc perlvar
    local $/ = ">";
    while(my $line = <SEQFILE>)
    {
        # the data will match a word, followed by a
        # newline, followed by another word
        # see perldoc perlretut and perlre
        if ($line =~ m/(\w+)\n(\w+)/s)
        {
            # the first word captured is the name
            my $name = $1;
            # the second word captured is the sequence
            my $sequence = $2;
            # add the sequence on to what ever is 
            # already there
            $seqref->{$name} .= $sequence;
        }
    }
    close SEQFILE;
}

sub write_file
{
    my $filename = shift;
    my $seqref = shift;

    open OUTPUT, ">$filename" or die "can't open $filename: $!";

    # write the sequences hash to the output file
    for my $key (sort keys %{$seqref})
    {
        print OUTPUT ">$key\n$seqref->{$key}\n" 
            or die "can't write: $!";
    }
    close OUTPUT or die "can't close $filename: $!";
}

__END__

[download]

In reply to Re: how to merge the files of DNA sequences? by beable
in thread how to merge the files of DNA sequences? by newperler

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.