I'd use a hash like this (code is documented with inline comments where necessary): 

use strict;
use warnings;
use Data::Dumper;

my %sequences;    # This hash will hold sequence ID's and the
                  # associated longest values.

while( defined( my $id = <DATA> ) ) {    # Read the ID from file.
    defined( my $sequence = <DATA> )     # Read the sequence.
        or die "Odd number of lines in DATA.\n";
    chomp for ( $id, $sequence );        # Chomp the input.
    $id =~ s/^>//;                       # Strip the > character
                                         # from the ID.
    if(
        exists( $sequences{ $id } ) and 
        length( $sequences{ $id } ) >= length( $sequence ) 
    ) {
        # Current sequence not longer. Skip to next record.
        next;
    } else {
        # Current sequence is longer.  Keep track of it.
        $sequences{ $id } = $sequence;
    }
}

#  Now %sequences contains all the longest strings for each ID.
#  Print the hash...
print Dumper \%sequences;

__DATA__
>protein1
ASFGTHTRHTHRHTHTRHTRHTR
>protein2
ERYRYTRYHTRHTGEFEWWFEEFFFFREFRGRE
>protein3
AWEERERGRGRGREGRGREGRRRRRRRRTTHTHTRHRHTRHTR
>protein2
AASEFEFEFE
>protein4
REYTRHTRGRVEVCREVR

[download]

Dave

In reply to Re: select strings with biggest length by davido
in thread select strings with biggest length by Anonymous Monk

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.