No, the split function is not a good way to do this trick. A regular expression is a better bet:

#!/usr/bin/perl
use strict;
use warnings;
use File::Copy; 
 
my $str1='MCCAALAPPMAATVGPESIWLWIGTIGMTLGTLYFVGRGRGVRDRKMQEFYIITIFITTI
+AAAMYFAMATGFGVT-------------EVMVG----DE---ALTIYWARYADWLFTTPLLLLDLSLLA
+GANRN----TIATLIG-LDVFMIG---T---GAIAALSST-PGTRIAWWAIST--GALL--ALLYVLVG
+TLSENARNRAPEVA--SLFGRLRNLVIALWFLYPVVWILGT---EGTFGILP--LYWETAAFMVLDLSA
+KVGFGVILLQSRSVLERVATPTAAPT';
my $str2='--OOOOOOOOOOOOOOOOMMMMMMMMMMMMMMMMMMMMMIIIIIIIIIIMMMMMMMMMMM
+MMMMMMMMMMOOOOO-------------OOOOO----OO---OOOOMMMMMMMMMMMMMMMMMMMMMII
+IIIII----MMMMMMM-MMMMMMM---M---MMMMMMOOO-OOOOMMMMMMMM--MMMM--MMMMMMMM
+MMIIIIIIIIIIII--IIIIMMMMMMMMMMMMMMMMMMMMO---OOO-OOOO--OOOMMMMMMMMMMMM
+MMMMMMMMMIIIIIIIIIIIII----';

while ($str2 =~ /(-+)/g) {
    my ($start, $end) = ($-[0], $+[0]);
    my $matchLen = $end - $start;
    
    next if substr($str1, $start, $matchLen) =~ /^-+$/;
    
    my $chIdx = $end == length($str2) ? $start - 1 : $end;
    
    substr ($str2, $start, $matchLen, substr($str2, $chIdx, 1) x $matc
+hLen);
}

print $str2;
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Prints:

OOOOOOOOOOOOOOOOOOMMMMMMMMMMMMMMMMMMMMMIIIIIIIIIIMMMMMMMMMMMMMMMMMMMMM
+OOOOO-------------OOOOO----OO---OOOOMMMMMMMMMMMMMMMMMMMMMIIIIIII----M
+MMMMMM-MMMMMMM---M---MMMMMMOOO-OOOOMMMMMMMM--MMMM--MMMMMMMMMMIIIIIIII
+IIII--IIIIMMMMMMMMMMMMMMMMMMMMO---OOOOOOOO--OOOMMMMMMMMMMMMMMMMMMMMMI
+IIIIIIIIIIIIIIII
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Modifying $str2 is resetting pos($str2), so you're doing a lot of unneeded work. Adding pos($str2) = $end; at the end of the loop addresses this issue.

Your script seems to make some additional assumptions that I cannot find in the original question. For example, for

my $str1='--M--CCA';
my $str2='-----OOO';
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your script prints OOOOOOOO while I would have thought it should be --O--OOO?

UPDATE: In order to avoid any confusion, the strings above are NOT part of the original question but examples I constructed assuming they could occur. The purpose of this was to highlight a situation where the proposed script would deliver something that violates the original requirements. Not sure the example is really relevant.

Good catch. It's a bug. The line:

next if substr($str1, $start, $matchLen) =~ /^-+$/;
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should be more like (untested):

next if ! matchLen || substr($str1, $start, $matchLen) !~ /[^-]/;
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Perl is the programming world's equivalent of English

Thanks so much!

No, the split function is not a good way to do this trick. A regular expression is a better bet:

FWIW, split function , same as match operator, both take a regular expression ;)

#!/usr/bin/perl

# http://perlmonks.org/?node_id=1123341

use strict;
use warnings;

my $str1='MCCAALAPPMAATVGPESIWLWIGTIGMTLGTLYFVGRGRGVRDRKMQEFYIITIFITTI
+AAAMYFAMATGFGVT-------------EVMVG----DE---ALTIYWARYADWLFTTPLLLLDLSLLA
+GANRN----TIATLIG-LDVFMIG---T---GAIAALSST-PGTRIAWWAIST--GALL--ALLYVLVG
+TLSENARNRAPEVA--SLFGRLRNLVIALWFLYPVVWILGT---EGTFGILP--LYWETAAFMVLDLSA
+KVGFGVILLQSRSVLERVATPTAAPT';

my $str2='--OOOOOOOOOOOOOOOOMMMMMMMMMMMMMMMMMMMMMIIIIIIIIIIMMMMMMMMMMM
+MMMMMMMMMMOOOOO-------------OOOOO----OO---OOOOMMMMMMMMMMMMMMMMMMMMMII
+IIIII----MMMMMMM-MMMMMMM---M---MMMMMMOOO-OOOOMMMMMMMM--MMMM--MMMMMMMM
+MMIIIIIIIIIIII--IIIIMMMMMMMMMMMMMMMMMMMMO---OOO-OOOO--OOOMMMMMMMMMMMM
+MMMMMMMMMIIIIIIIIIIIII----';

my ($last) = $str2 =~ /.*(\w)/; # find letter for ending -'s

tr/\0-/-=/, s/=(?=\W*(\w?))/ $1 || $last /ge
  for my $answer = $str1 =~ tr/A-Z/\0/r ^ $str2;

print "$answer\n";
[download]

Explanation provided on request :)

See also this thread for a very similar, though not identical, problem. Also, Hello! to your perl teacher.

#! /usr/bin/perl

sub ano1 {
    my ($str1, $str2) = @_;

    my ($last) = $str2 =~ /.*(\w)/;

    tr/\0-/-=/, s/=(?=\W*(\w?))/ $1 || $last /ge
      for my $answer = $str1 =~ tr/A-Z/\0/r ^ $str2;

    $answer;
}

sub ano2 {
    my ($x, $y) = @_;
    $y &= ($y =~ tr/-\0-\377/\0\377/r) | ($x =~ tr/-\0-\377/\377\0/r);
    $y =~ s/(\0+)(.)/$2 x (1 + length $1)/eg;
    $y =~ s/(.)(\0+)$/$1 x (1 + length $2)/er;
}

chomp (our ($str1, $str2) = <DATA>);

use Benchmark 'cmpthese';
cmpthese -5, {
    ano1 => q( ano1 $str1, $str2 ),
    ano2 => q( ano2 $str1, $str2 ),
};

__DATA__
MCCAALAPPMAATVGPESIWLWIGTIGMTLGTLYFVGRGRGVRDRKMQEFYIITIFITTIAAAMYFAMAT
+GFGVT-------------EVMVG----DE---ALTIYWARYADWLFTTPLLLLDLSLLAGANRN----T
+IATLIG-LDVFMIG---T---GAIAALSST-PGTRIAWWAIST--GALL--ALLYVLVGTLSENARNRA
+PEVA--SLFGRLRNLVIALWFLYPVVWILGT---EGTFGILP--LYWETAAFMVLDLSAKVGFGVILLQ
+SRSVLERVATPTAAPT
--OOOOOOOOOOOOOOOOMMMMMMMMMMMMMMMMMMMMMIIIIIIIIIIMMMMMMMMMMMMMMMMMMMMM
+OOOOO-------------OOOOO----OO---OOOOMMMMMMMMMMMMMMMMMMMMMIIIIIII----M
+MMMMMM-MMMMMMM---M---MMMMMMOOO-OOOOMMMMMMMM--MMMM--MMMMMMMMMMIIIIIIII
+IIII--IIIIMMMMMMMMMMMMMMMMMMMMO---OOO-OOOO--OOOMMMMMMMMMMMMMMMMMMMMMI
+IIIIIIIIIIII----
[download]

Sigh, this is too crazy. I give up, and I'll go back to golf!

This runs faster as a one-liner than as multiple lines. :(

Also tr/A-Z/\0/r is faster than tr/-/\0/cr It makes no sense :(

sub ano1 { (pop ^ pop =~ tr/A-Z/\0/r) =~ tr/\0-/-=/r =~ s/(=+(\w))/$2 
+x length $1/ger =~ s/((.)=+)$/$2 x length $1/er }
[download]