Perl：返回字符串的最高百分比匹配

Question

我有一个DNA序列，例如ATCGATCG。我也有格式化的DNA序列的数据库，如下所示：

>Name of sequence1 
SEQUENCEONEEXAMPLEGATCGATC 
>Name of sequence2 
SEQUENCETWOEXAMPLEGATCGATC 

（所以奇数行包含名称和偶数行包含一个序列） 目前，我寻找我的序列之间的完美匹配在如下数据库序列（假设所有的变量声明）：

my $name; 
my $seq; 
my $returnval = "The sequence does not match any in database"; 
open (my $database, "<", $db1) or die "Can't find db1"; 
until (eof $database){ 
    chomp ($name = <$database>); 
    chomp ($seq = <$database>); 
    if (
     index($seq, $entry) != -1 
     || index($entry, $seq) != -1 
    ) { 
     $returnval = "The sequence matches: ". $name; 
     last; 
    } 
} 
close $database; 

有什么办法，我返回比例最高的匹配序列的名称以及匹配百分比有入口和之间数据库中的序列？

Answer 1

String::Similarity将字符串之间的相似性返回为0和1之间的值，0完全不相似，1完全相同。

my $entry = "AGGUUG" ; 
my $returnval; 
my $name; 
my $seq; 
my $currsim; 
my $highestsim = 0; 
my $highestname; 
open (my $database, "<", $db1) or die "Can't find db1"; 
until (eof $database){ 
    chomp ($name = <$database>); 
    chomp ($seq = <$database>); 
    $currsim = similarity $entry, $seq, $highestsim; 
    if ($currsim > $highestsim) { 
     $highestsim = $currsim; 
     $highestname = $name; 
    } 
} 
$highestsim = $highestsim * 100; 
my @names = split(/>/, $highestname); 
$returnval = "This sequence matches " . $names[1] . " the best with " . $highestsim . "% similarity"; 
close $database;