This approach follows your statement of the problem. 
use strict;
use warnings;
use List::MoreUtils qw(first_index);
my $sample = \do{my $raw =
    "> gi|11SB_CUCMA Train|1 21\n"
   ."MARSSLFTFLCLAVFINGCLSQIEQQSPWEFQGS\n"
   ."EVWQQHRYQSPRACRLENLRAQDPVRLLLPGFSNAPKLIFV\n"
   ."AQGFGIRGIAIPGCAETYQT\n"
   ."SSSSSSSSSSSSSSSSSSSSS....................\n"
   ."...........................\n"
   .".................\n"
   ."..........\n"
   ."> gi|1A43_HUMAN Train|1 24\n"
   ."MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFYTSVSRPG\n"
   ."RGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEG"
        ."PEYWSQTDRANLGTLRGYYNQSEDGSHTIQR\n"
   ."MYGCDVGPDGRFLRGYQQDAYDGKDYIALNEDLRS"
        ."WTAADMAAQITQRKWETAHEAE\n"
   ."SSSSSSSSSSSSSSSSSSSSSSSS..........."
        ."...................................\n"
   ."...........................................\n"
   .".............\n"
   ."..........................................\n"
};
open my $SAMPLE, '<', $sample;
while (my $block = do{local $/ = "\n>"; <$SAMPLE>}) { 
    $block =~ s/\n>\z//;
    $block =~ s/\A([^>])(.*?)$/>$1$2/ms;
    my @lines = split /\n/, $block;
    my $i = first_index {$_ =~ /\./} @lines;
    $" = q();
    print $lines[0], "\n"
         ."@lines[1..$i-1]\n"
         ."@lines[$i..$#lines]\n";
}

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Bill

In reply to Re: Help in joining these lines by BillKSmith
in thread Help in joining these lines by Anonymous Monk

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