These look very similar, the similarity is just obscured by some comments. So let's remove the comments, and find out what's the difference:

diff -u a b
--- a   2009-05-05 19:55:21.000000000 +0200
+++ b   2009-05-05 19:54:44.000000000 +0200
@@ -1,7 +1,7 @@
-sub blast_parse{
+sub blast_hd_parse{
     my($maid,$maid_dir) = @_;
-    my $url_hu = "http://hu_seq/";
-    my $hu = get($url_hu.$maid);
+    my $url_hd = "http://hd_seq/";
+    my $hd = get($url_hd.$maid);
     my $ltvec_small = $maid_dir.$maid."Ltvec_small.fa";
     open ($hu);
     my $seq=<$in>;
@@ -9,7 +9,8 @@
     open ($hu, ">".$maid.".fa");
     print $hu_fa ">$maid\n$seq";
     close($hu_fa);
-    my $command = "bl2seq -p blastn -i $ltvec_small -j $hu_fa -F F -D
+ 1";
+    
+    my $command = "bl2seq -p blastn -i $ltvec_small -j $hd_fa -F F -D
+ 1";
     print $command,"\n";
     open OUTPUT, '>',  "$maid_dir\\".$maid."_bl2seq.out" ;
     STDOUT->fdopen( \*OUTPUT, 'w');
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(A graphical diff utility like gvimdiff is also very helpful).

The first difference is the sub name, which we'll ignore for now. The second difference is a differently named variable, and a different constant value. Let's just name the variables $url in both subs, and assume that $hd is actually a typo (it's not used anywhere below in the code).

Then you can clean up your code a bit (do you use strict;? you know you should!) and you'll find that the subs are identical, except for the different URL, which can be provided as another parameter.