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'AF035737 Homo sapiens general transcription factor 2-I (GTF2I) mRNA, 
+complete.'

/Homo sapiens/  will match
/^Homo sapiens/ will not

sub filter_by_Species()
# Don't use prototypes unless you NEED them. And even then, you probab
+ly don't.
...
    show_Output($boolean, $z, @elements);
# boolean ALWAYS equal 0. Why not just pass 0?

sub filter_by_Species
{
...

print'</TABLE><BR><BR>';
}