I have a file given below: 

AAF88103.1 zinc finger protein 226 [Homo sapiens]MNMFKEAVTFKDVAVAFTEEE
+LGLLGPAXRKLYRD
VMVENFRNLLSVGHPPFKQDVSPIERNEQLWIMTTATRRQGNLGEKNQSKLITVQDRESEEELSCWQIWQ
+QIANDLT
RCQDSMINNSQCHKQGDFPYQVGTELSIQISEDENYIVNKADGPNNTGNPEFPILRTQDSWRKTFLTESQ
+RLNRDQQI
SIKNKLCQCKKGVDPIGWISHHDGHRVHKSEKSYRPNDYEKDNMKILTFDHNSMIHTGQKSYQCNECKKP
+FSDLSSF
DLHQQLQSGEKSLTCVERGKGFCYSPVLPVHQKVHVGEKLKCDECGKEFSQGAHLQTHQKVHVIEKPYKC
+KQCGKGF
SRRSALNVHCKVHTAEKPYNCEECGRAFSQASHLQDHQRLHTGEKPFKCDACGKSFSRNSHLQSHQRVHT
+GEKPYK
CEECGKGFICSSNLYIHQRVHTGEKPYKCEECGKGFSRPSSLQAHQGVHTGEKSYICTVCGKGFTLSSNL
+QAHQRVHTG
EKPYKCNECGKSFRRNSHYQVHLVVHTGEKPYKCEICGKGFSQSSYLQIHQKAHSIEKPFKCEECGQGFN
+QSSRLQIHQL
IHTGEKPYKCEECGKGFSRRADLKIHCRIHTGEKPYNCEECGKVFRQASNLLAHQRVHSGEKPFKCEECG
+KSFGRSAHLQ
AHQKVHTGDKPYKCDECGKGFKWSLNLDMHQRVHTGEKPYKCGECGKYFSQASSLQLHQSVHTGEKPYKC
+DVCGKVF
SRSSQLQSHQRVHTGEKPYKCEICGKSFSWRSNLTVHHRIHVGDKSYKSNRGGKNIRESTQEKKSIK

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I want to look for a pattern i.e: (CDECGKEFSQGAHLQTHQKVH) which should be hardcoded in the program like the code i have written below:

  open FILE1, "file,fasta" or die;

while (my $line=<FILE1>) {

chomp $line;

}

if ($line =~ /CDECGKEFSQGAHLQTHQKVH/) {
    print "The protein contains the domain";
}else{
    print "The protein doesn't contain the domain";
}

[download]

Is this the correct way of doing it?

In reply to Finding pattern in a file by shabird

Title:
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