($line =~ /^>(\S+)\s*(.*)/ ); # what is exactly doing?

this line search: a beginning of line, followed by at least one letter or digit that are captured for reuse later as ID, followed or not with one or some white spaces, followed or not by anything. Anything is captured also so you can pass this to a second variable later (Description). Whitespaces and the description block are optional

i.e, this

blablabla blobloblo #OK

blabla #OK

b #OK

   blabla #NOT, note the whitespaces before
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Now, what I need it to do is, add more strings. I need two extra strings.

my $first_extra_string = 'I am a cow';
my $second_extra_string = 'moo too';
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How can add more $ to it, such as acession numbers?

my $adding_more_dollar_signs = "I am rocowfeller, I have a lot of \$\$\$\$\$!";

Maybe you should explain better what you want to do exactly?

something like this?

($line =~ /^>(\S+)\s*(.*)\s*(.*)\s*(.*)/ );
my $daisy_cow = $3;
my $shawn_the_sheep = $4;
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