Finding Palindromes(perfect palindromes) in more than one protein sequences using perl

Question

I am a newbie in Perl (Regular Expressions). I need aa example on how to write a program for finding out palindromes (perfect) in more than one protein sequences (let it be 4 sequence with 200 amino acids in number, in a file) I have to filter out, the palindromes and the position of palindromes present in the sequences.

>TRE|Q47404|Q47404 (409 AA) Glycosyl transferase [Escherichia coli]
MIFDASLKKLRKLFVNPIGFFRDSWFFNSKNKAEELLSPLKIKSKNIFIVAHLGQLKKAE
LFIQKFSRRSNFLIVLATKKNTEMPRLILEQMNKKLFSSYKLLFIPTEPNTFSLKKVIWF
YNVYKYIVLNSKAKDAYFMSYAQHYAIFIWLFKKNNIRCSLIEEGTGTYKTEKKKPLVNI
NFYSWIINSIILFHYPDLKFENVYGTFPNLLKEKFDAKKIFEFKTIPLVKSSTRMDNLIH

>TRE|O06435|O06435 (492 AA) SynE [Neisseria meningitidis]
MLQKIRKALFHPKKFFQDSQWFATPLFSSFAPKSNLFIISTFAQLNQAHSLTKMQKLKNN
LLVILYTTQNMKMPKLIQKSVDKELFSVTYMFELPRKPGIVSPKKFLYIQRGYKKLLKTI
QPAHLYVMSFAGHYSSLLSLAKKMNITTHLVEEGTATYAPLLESFTYKPTKFEQRFVGNN
LHQKGYFDKFDILHVAFPEYAKKIFNANEYHRFFAHSGGISTSQSIAKIQDKYRISQNDY
IFVSQRYPVSDEVYYKTIVETLNQMSLRIEGKIFIKLHPKEMENKNIMSLFLNMVTINPR

>TRE|Q8VRL9|Q8VRL9 (492 AA) SiaD [Neisseria meningitidis]
MLQKIRKALFHPKKFFQDSQWFATPLFSSFAPKSNLFIISTFAQLNQAHSLTKMQKLKNN
LLVILYTTQNMKMPKLIQKSVDKELFSVTYMFELPRKPGIVSPKKFLYIQRGYKKLLKTI
QPAHLYVMSFAGHYSSLLSLAKKMNITTHLVEEGTATYAPLLESFTYKPTKFEQRFVGNN
LHQKGYFDKFDILHVAFPEYAKKIFNANEYHRFFAHSGGISTSQSIAKIQDKYRISQNDY

I need the output of perfect palindromes in this and also their positions. I have gone through many articles, but couldn't get any better idea. Please suggest me some techniques and programs for this.

Answer 1

There are three regex features that are required for this challenge:

1. perlretut - Recursive Patterns — To find palindromes

2. perlretut - Positive Lookahead Assertions — To find matches that overlap

3. perlretut - Position Information — To determine where the matches are in the string.

Putting these together gives this result:

use strict;
use warnings;

my $pp = qr/(?: (\w) (?1) \g{-1} | \w? )/ix;

local $/ = '';

while (<DATA>) {
    chomp;
    my ($header, @lines) = split "\n";
    my $data = join '', @lines;

    print "$header\n$data\n";

    while ($data =~ /(?=($pp))/g) {
        print "$-[0] - $1\n" if length($1) > 2;
    }
}

__DATA__
>TRE|Q47404|Q47404 (409 AA) Glycosyl transferase [Escherichia coli]
MIFDASLKKLRKLFVNPIGFFRDSWFFNSKNKAEELLSPLKIKSKNIFIVAHLGQLKKAE
LFIQKFSRRSNFLIVLATKKNTEMPRLILEQMNKKLFSSYKLLFIPTEPNTFSLKKVIWF
YNVYKYIVLNSKAKDAYFMSYAQHYAIFIWLFKKNNIRCSLIEEGTGTYKTEKKKPLVNI
NFYSWIINSIILFHYPDLKFENVYGTFPNLLKEKFDAKKIFEFKTIPLVKSSTRMDNLIH

>TRE|O06435|O06435 (492 AA) SynE [Neisseria meningitidis]
MLQKIRKALFHPKKFFQDSQWFATPLFSSFAPKSNLFIISTFAQLNQAHSLTKMQKLKNN
LLVILYTTQNMKMPKLIQKSVDKELFSVTYMFELPRKPGIVSPKKFLYIQRGYKKLLKTI
QPAHLYVMSFAGHYSSLLSLAKKMNITTHLVEEGTATYAPLLESFTYKPTKFEQRFVGNN
LHQKGYFDKFDILHVAFPEYAKKIFNANEYHRFFAHSGGISTSQSIAKIQDKYRISQNDY
IFVSQRYPVSDEVYYKTIVETLNQMSLRIEGKIFIKLHPKEMENKNIMSLFLNMVTINPR

>TRE|Q8VRL9|Q8VRL9 (492 AA) SiaD [Neisseria meningitidis]
MLQKIRKALFHPKKFFQDSQWFATPLFSSFAPKSNLFIISTFAQLNQAHSLTKMQKLKNN
LLVILYTTQNMKMPKLIQKSVDKELFSVTYMFELPRKPGIVSPKKFLYIQRGYKKLLKTI
QPAHLYVMSFAGHYSSLLSLAKKMNITTHLVEEGTATYAPLLESFTYKPTKFEQRFVGNN
LHQKGYFDKFDILHVAFPEYAKKIFNANEYHRFFAHSGGISTSQSIAKIQDKYRISQNDY

Outputs:

>TRE|Q47404|Q47404 (409 AA) Glycosyl transferase [Escherichia coli]
MIFDASLKKLRKLFVNPIGFFRDSWFFNSKNKAEELLSPLKIKSKNIFIVAHLGQLKKAELFIQKFSRRSNFLIVLATKKNTEMPRLILEQMNKKLFSSYKLLFIPTEPNTFSLKKVIWFYNVYKYIVLNSKAKDAYFMSYAQHYAIFIWLFKKNNIRCSLIEEGTGTYKTEKKKPLVNINFYSWIINSIILFHYPDLKFENVYGTFPNLLKEKFDAKKIFEFKTIPLVKSSTRMDNLIH
6 - LKKL
29 - KNK
40 - KIK
42 - KSK
46 - IFI
66 - SRRS
86 - LIL
123 - YKY
131 - KAK
146 - IFI
164 - GTG
165 - TGT
172 - KKK
178 - NIN
211 - KEK
220 - FEF
>TRE|O06435|O06435 (492 AA) SynE [Neisseria meningitidis]
MLQKIRKALFHPKKFFQDSQWFATPLFSSFAPKSNLFIISTFAQLNQAHSLTKMQKLKNNLLVILYTTQNMKMPKLIQKSVDKELFSVTYMFELPRKPGIVSPKKFLYIQRGYKKLLKTIQPAHLYVMSFAGHYSSLLSLAKKMNITTHLVEEGTATYAPLLESFTYKPTKFEQRFVGNNLHQKGYFDKFDILHVAFPEYAKKIFNANEYHRFFAHSGGISTSQSIAKIQDKYRISQNDYIFVSQRYPVSDEVYYKTIVETLNQMSLRIEGKIFIKLHPKEMENKNIMSLFLNMVTINPR
26 - FSSF
55 - KLK
70 - MKM
114 - KLLK
135 - SLLS
137 - LSL
154 - TAT
205 - NAN
220 - STS
222 - SQS
271 - KIFIK
272 - IFI
280 - EME
283 - NKN
289 - LFL
>TRE|Q8VRL9|Q8VRL9 (492 AA) SiaD [Neisseria meningitidis]
MLQKIRKALFHPKKFFQDSQWFATPLFSSFAPKSNLFIISTFAQLNQAHSLTKMQKLKNNLLVILYTTQNMKMPKLIQKSVDKELFSVTYMFELPRKPGIVSPKKFLYIQRGYKKLLKTIQPAHLYVMSFAGHYSSLLSLAKKMNITTHLVEEGTATYAPLLESFTYKPTKFEQRFVGNNLHQKGYFDKFDILHVAFPEYAKKIFNANEYHRFFAHSGGISTSQSIAKIQDKYRISQNDY
26 - FSSF
55 - KLK
70 - MKM
114 - KLLK
135 - SLLS
137 - LSL
154 - TAT
205 - NAN
220 - STS
222 - SQS