Perfect Matchings and RNA Secondary Structures


TITLE

AUTHOR

code

=begin code :lang<raku>
use v6;



my $default-input = q:to/END/;
    >Rosalind_23
    AGCUAGUCAU
    END

sub MAIN($input-file = Nil) {
    my $input = $input-file ?? $input-file.IO.slurp !! $default-input;
    my $rna = join '', grep /^ <[ACGU]>+ $/, $input.lines;

    say [*] map { [*] 1 .. $rna.comb(/$_/).elems }, <U C>;
}

# vim: expandtab shiftwidth=4 ft=perl6

=end code


root

Counting Disease Carriers


afrq-grondilu.pl

Introduction to Alternative Splicing


aspc-grondilu.pl

Consensus and Profile


cons-grondilu.pl

Comparing Spectra with the Spectral Convolution


conv-grondilu.pl

Creating a Character Table from Genetic Strings


cstr-grondilu.pl

Creating a Character Table


ctbl-grondilu.pl

Introduction to Protein Databases


dbpr-grondilu.pl

Counting DNA Nucleotides


dna-gerdr.pl

dna-grondilu.pl

Enumerating Unrooted Binary Trees


eubt-grondilu.pl

Expected Number of Restriction Sites


eval-grondilu.pl

Rabbits and Recurrence Relations


fib-grondilu.pl

Mortal Fibonacci Rabbits


fibd-grondilu.pl

Computing GC Content


gc-gerdr.pl

Overlap Graphs


grph-grondilu.pl

Counting Point Mutations


hamm-grondilu.pl

Calculating Expected Offspring


iev-grondilu.pl

Independent Segregation of Chromosomes


indc-grondilu.pl

Mendel's First Law


iprb-grondilu.pl

Finding Disjoint Motifs in a Gene


itwv-grondilu.pl

Finding a Shared Spliced Motif


lcsq-grondilu.pl

Independent Alleles


lia-grondilu.pl

lrep-grondilu-p5.pl

Maximum Matchings and RNA Secondary Structures


mmch-grondilu.pl

Finding a Protein Motif


mprt-grondilu.pl

Inferring mRNA from Protein


mrna-grondilu.pl

Distances in Trees


nwck-grondilu.pl

Open Reading Frames


orf-grondilu.pl

Partial Permutations


pper-grondilu.pl

Introduction to Random Strings


prob-grondilu.pl

Quartets


qrt-grondilu.pl

README.md

Complementing a Strand of DNA


revc-gerdr.pl

Transcribing DNA into RNA


rna-gerdr.pl

Matching Random Motifs


rstr-grondilu.pl

Sex-Linked Inheritance


sexl-grondilu.pl

Using the Spectrum Graph to Infer Peptides


sgra-grondilu.pl

Inferring Protein from Spectrum


spec-grondilu.pl

Finding a Spliced Motif


sseq-grondilu.pl

Finding a Motif in DNA


subs-grondilu.pl

Encoding Suffix Trees


suff-grondilu.pl

Transitions and Transversions


tran-grondilu.pl

Introduction to Pattern Matching


trie-grondilu.pl

para

L<Examples| file:../examples/index.podlite>


L<Download |file:../download/index.podlite>


React

=begin React :component<HeaderCol> :id<menu> 
=para L<Documentation|/doc/introduction>
=para L<Modules| /mods>
=para L<Examples| file:../examples/index.podlite>
=para L<Download |file:../download/index.podlite>
=para L<About|file:../about/index.podlite>
=para 🔍 K<⌘K>/K<ctrl-K>
=end React


HEADER

FOOTER

=begin code :lang<raku>
use v6;



sub pper($n, $k) { [*] $n-$k+1 .. $n }

sub MAIN(Str $input = "21 7") {
    say pper(| $input.split: " ") % 1_000_000;
}

# vim: expandtab shiftwidth=4 ft=perl6

=end code


pmch-grondilu.pl

>Rosalind_99
AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAAGCCTGAATGATCCGAGTAGCATCTCAG


MLLGSFRLIPKETLIQVAGSSPCNLS
M
MGMTPRLGLESLLE
MTPRLGLESLLE


=begin code :lang<raku>
use v6;



constant DNA-codon = Hash.new: <
    TTT F      CTT L      ATT I      GTT V
    TTC F      CTC L      ATC I      GTC V
    TTA L      CTA L      ATA I      GTA V
    TTG L      CTG L      ATG M      GTG V
    TCT S      CCT P      ACT T      GCT A
    TCC S      CCC P      ACC T      GCC A
    TCA S      CCA P      ACA T      GCA A
    TCG S      CCG P      ACG T      GCG A
    TAT Y      CAT H      AAT N      GAT D
    TAC Y      CAC H      AAC N      GAC D
    TAA Stop   CAA Q      AAA K      GAA E
    TAG Stop   CAG Q      AAG K      GAG E
    TGT C      CGT R      AGT S      GGT G
    TGC C      CGC R      AGC S      GGC G
    TGA Stop   CGA R      AGA R      GGA G
    TGG W      CGG R      AGG R      GGG G
>;

my $default-input = "AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAAGCCTGAATGATCCGAGTAGCATCTCAG";

sub revc($dna) {
    $dna.comb.reverse.join.trans:
    [<A C T G>] => [<T G A C>]
}

sub orf($dna) {
    my %match;
    my @match = (gather for $dna, revc $dna {
        take .match: rx/ ATG [ <[ACGT]>**3 ]*? <before TAA|TAG|TGA> /, :overlap;
    })>>.list.flat;

    %match{
        [~] map { DNA-codon{$_} }, .match: rx/ <[ACGT]>**3 /, :g
    }++ for @match;

    return %match.keys.sort;
}

sub MAIN(Str $input = $default-input) {
    .say for orf $input;
}

# vim: expandtab shiftwidth=4 ft=perl6

=end code


The Raku Knowledge Base


=begin React :component<HeaderCol> :id<footer>  
=begin nested :!nested
=item1 B<Language>
    =item2 L<Get started|file:../getting-started/getting-started.podlite>
    =item2 L<Why Raku?|/doc/language/faq#Why-should-I-learn-Raku-What's-so-great-about-it>
    =item2 L<Try Raku|https://glot.io/new/raku>
    =item2 L<Raku cheat sheet|https://github.com/Raku/mu/blob/master/docs/Perl6/Cheatsheet/cheatsheet.txt>
    =item2 L<empty|#>
    =item2 L<empty|#>
    =item2 L<empty|#>
    =item2 L<Raku on Exercism|https://exercism.org/tracks/raku>
    =item2 L<Wikipedia|https://en.wikipedia.org/wiki/Raku_(programming_language)>
    =item2 L<empty|#>
    =item2 L<empty|#>
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    =item2 L<Language References|file:../doc/reference.podlite>
    =item2 L<Type Reference| file:../doc/types.podlite>
    =item2 L<Miscellaneous| file:../doc/miscellaneous.podlite>
    =item2 L<FAQs (Frequently Asked Questions)|/doc/language/faq>
    =item2 L<Community|/doc/language/community>
    =item2 L<The list of all documents|file:../doc/index.podlite>

=item1 B<Resources>
    =item2 L<The Raku Guide|https://raku.guide/>
    =item2 L<Books |https://perl6book.com/>
    =item2 L<Rosetta Code | https://www.raku.org/community/rosettacode>

=end nested
=begin nested :!nested

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    =item2 L<Download | file:../download/index.podlite>
    =item2 L<empty|#>
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=item1 B<Learning>
    =item2 L<The Raku Guide|https://raku.guide/>
    =item2 L<Wikibook |https://en.wikibooks.org/wiki/Raku_Programming>
    =item2 L<Books |https://perl6book.com/>
    =item2 L<Rosetta Code | https://www.raku.org/community/rosettacode>
    =item2 L<Learn Raku in Y minutes|https://learnxinyminutes.com/docs/raku/>
    =item2 L<Golfing |https://github.com/AlexDaniel/raku-golf-cheatsheet>
=end nested
=begin nested :!nested

=item1 B<Explore>
    =item2 L<Raku Blog Aggregator|https://planet.raku.org/>
    =item2 L<Rakudo Weekly|https://rakudoweekly.blog/>
    =item2 L<The Weekly Challenge |https://perlweeklychallenge.org/>
    =item2 L<Raku Advent Calendar|https://raku-advent.blog/>
    =item2 L<empty|#>
    =item2 L<empty|#>
    =item2 L<empty|#>
    =item2 L<empty|#>
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=end nested
=end React


=begin React :component<CookieConsent> :id<CookieConsent> :buttonCaption("Got it!")
=para
This website uses cookies for analytics.
=end React


AUTHOR

See Also