Hello! I hope my problem is more complicated than the title suggests. I need to compare a series of 100 sequences with the original and the program should give me one number of identities. For example:

Original sequence: ATCGGGACG 
Stream 0:          TCGTCAGCG
Sequence 1:        ATGCGAAAA

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Then the program should print:

The sequence 0 has 2 identities
The sequence 1 has 4 identities

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My code requires a file containing the original sequence (you will note this at the biginning, where it says: "original.FASTA") so I don't know if you can work without it. Thanks already.

#!/usr/bin/perl -w
#Lectura de archivo de secuencias
$secuencia = 'original.FASTA';
#Abrir el archivo
open (SECUENCIA, $secuencia);
#Leer la secuencia
@secuencia = <SECUENCIA>;
close SECUENCIA;
#Eliminar la línea de título.
$secuencia[0]="";
#print "Esta es la secuencia:\n\n";
#print @secuencia;
#Convertir el arreglo a una variable, con el comando join.
$DNA = join('',@secuencia);
#Concatenar las líneas:
chomp @secuencia;
$DNA =~ s/\n//g; #Quita los saltos de línea.
$DNA =~ s/\s//g;

print "La secuencia original es: \n\n",$DNA,"\n\n";

#Secuencias aleatorias
$test="ACGT";
@DNA=split("",$test);

for ($j=0; $j < 100; ++$j){
    $salida="";
    for ($i=0; $i < 541; ++$i){
        $random=rand(length($test));
        $salida=$salida.$DNA[$random];
    }
    print ">Secuencia_$j\n$salida\n";
}

exit;

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In reply to Compare two variables by dmunoze

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