This looks like FASTA format. I'd say you're on the right track by changing $/; however, it's better to localise the change in an anonymous block and let Perl return it to its previous value (rather than hard-coding your guess of what it was). I typically use: local $/ = "\n>".

If you have Perl v5.14 or higher, you can code it like this:

#!/usr/bin/env perl

use 5.014;
use strict;
use warnings;

{
    local $/ = "\n>";

    while (<DATA>) {
        chomp;
        my ($top, $seq) = split /\n/, $_, 2;
        print '>' unless $. == 1;
        say $top;
        say $seq =~ y/\n//dr;
    }
}

__DATA__
> gi|11SB_CUCMA Train|1 21
MARSSLFTFLCLAVFINGCLSQIEQQSPWEFQGS
EVWQQHRYQSPRACRLENLRAQDPVRLLLPGFSNAPKLIFV
AQGFGIRGIAIPGCAETYQT
SSSSSSSSSSSSSSSSSSSSS....................
...........................
.................
..........
> gi|1A43_HUMAN Train|1 24
MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFYTSVSRPG
RGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWSQTDRANLGTLRGYYNQSEDGSHTIQ
+R
MYGCDVGPDGRFLRGYQQDAYDGKDYIALNEDLRSWTAADMAAQITQRKWETAHEAE
SSSSSSSSSSSSSSSSSSSSSSSS..............................................
+...........................................
.............
..........................................
[download]

Output:

> gi|11SB_CUCMA Train|1 21
MARSSLFTFLCLAVFINGCLSQIEQQSPWEFQGSEVWQQHRYQSPRACRLENLRAQDPVRLLLPGFSNAP
+KLIFVAQGFGIRGIAIPGCAETYQTSSSSSSSSSSSSSSSSSSSSS.......................
+...................................................
> gi|1A43_HUMAN Train|1 24
MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRME
+PRAPWIEQEGPEYWSQTDRANLGTLRGYYNQSEDGSHTIQRMYGCDVGPDGRFLRGYQQDAYDGKDYIA
+LNEDLRSWTAADMAAQITQRKWETAHEAESSSSSSSSSSSSSSSSSSSSSSSS................
+.....................................................................
+...........................................................
[download]

If you only have v5.10 or v5.12, the 'r' modifier for transliteration is unavailable (see Non-destructive substitution in perl5140delta: Regular Expressions) and you'll need an extra line of code.

#!/usr/bin/env perl

use 5.010;
use strict;
use warnings;

{
    local $/ = "\n>";

    while (<DATA>) {
        chomp;
        my ($top, $seq) = split /\n/, $_, 2;
        print '>' unless $. == 1;
        say $top;
        $seq =~ y/\n//d;
        say $seq;
    }
}
[download]

If you're working with older Perl versions, 'say' is unavailable (see perl5100delta: say()) and you'll need to hard-code line endings.

#!/usr/bin/env perl

use strict;
use warnings;

{
    local $/ = "\n>";

    while (<DATA>) {
        chomp;
        my ($top, $seq) = split /\n/, $_, 2;
        print '>' unless $. == 1;
        print "$top\n";
        $seq =~ y/\n//d;
        print "$seq\n";
    }
}
[download]

All of these versions of the code produce the same output (given the same __DATA__).

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