How to search motif pattern in FASTA sequences using Perl hash?

Here is a simple Perl script to search for motif patterns in a large FASTA file with multiple sequences.

Suppose, your multifasta file is “input.fa”, in which you want to search for the motif patterns.

Case-I Search a pre-defined motif pattern.

use strict 'vars';
use warnings;

my $regex = "motif_pattern";

my %sequences = %{ read_fasta_file( 'input.fa' ) };
open( STDOUT, ">", "output.fa" ) or die!$;
foreach my $header ( keys %sequences ) {
    if ( $sequences{$header} =~ /$regex/ ) {
		print $header, "\n";
        print $sequences{$header}, "\n";
    }
}

sub read_fasta_file {
    my $filename = shift;
    my $current_header = '';
    my %sequences;
    open FILE, "$filename" or die $!;
	    while ( my $line = <FILE>) {
        chomp $line;
        if ( $line =~ /^(>.*)$/ ) {
            $current_header  = $1;
        }

        elsif ( $line !~ /^\s*$/ ) { # skip blank lines
            $sequences{$current_header} .= $line;
        }
    }
    close FILE or die $!;

    return \%sequences;
}

Case-II Search a user input motif pattern.

use strict 'vars';
use warnings;

print "Enter a motif pattern to search";
my $regex = ;

my %sequences = %{ read_fasta_file( 'input.fa' ) };
open( STDOUT, ">", "output.fa" ) or die!$;
foreach my $header ( keys %sequences ) {
    if ( $sequences{$header} =~ /$regex/ ) {
		print $header, "\n";
        print $sequences{$header}, "\n";
    }
}

sub read_fasta_file {
    my $filename = shift;
    my $current_header = '';
    my %sequences;
    open FILE, "$filename" or die $!;
	    while ( my $line = <FILE> ) {
        chomp $line;
        if ( $line =~ /^(>.*)$/ ) {
            $current_header  = $1;
        }

        elsif ( $line !~ /^\s*$/ ) { # skip blank lines
            $sequences{$current_header} .= $line;
        }
    }
    close FILE or die $!;

    return \%sequences;
}

Save this script with .pl extension and run as perl script.pl in terminal (in Linux) or in command prompt (in Windows).