Comparing Spectra with the Spectral Convolution


TITLE

AUTHOR

186.07931 287.12699 548.20532 580.18077 681.22845 706.27446 782.27613 968.35544 968.35544
101.04768 158.06914 202.09536 318.09979 419.14747 463.17369


code

=begin code :lang<raku>
use v6;



my $a = "186.07931 287.12699 548.20532 580.18077 681.22845 706.27446 782.27613 968.35544 968.35544";
my $b = "101.04768 158.06914 202.09536 318.09979 419.14747 463.17369";

my %conv; %conv{$_}++ for $a.split(/\s+/) X- $b.split(/\s+/);
.say for max(:by(*.value), %conv).kv.reverse;

# 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

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

Perfect Matchings and RNA Secondary Structures


pmch-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

ATGCTACC
CGTTTACC
ATTCGACC
AGTCTCCC
CGTCTATC


=begin code :lang<raku>
use v6;



my @default-data = qw:to/END/;
    ATGCTACC
    CGTTTACC
    ATTCGACC
    AGTCTCCC
    CGTCTATC
    END

sub MAIN($input-file = Nil) {
    my @input = $input-file ?? $input-file.IO.lines !! @default-data;
    my @dna = map { [.comb] }, @input;
    my @c = @dna[0][];

    for ^@c -> $c {
        my @line = map { +so .[$c] eq @c[$c] }, @dna;
        say @line.join if 1 < ([+] @line) < @dna-1;
    }
}

# vim: expandtab shiftwidth=4 ft=perl6

=end code


conv-grondilu.pl

ATCCAGCT
GGGCAACT
ATGGATCT
AAGCAACC
TTGGAACT
ATGCCATT
ATGGCACT


ATGCAACT
A: 5 1 0 0 5 5 0 0
C: 0 0 1 4 2 0 6 1
G: 1 1 6 3 0 1 0 0
T: 1 5 0 0 0 1 1 6


=begin code :lang<raku>
use v6;



my @default-data = qw{
    ATCCAGCT
    GGGCAACT
    ATGGATCT
    AAGCAACC
    TTGGAACT
    ATGCCATT
    ATGGCACT
};

my \N = @default-data.pick.chars;

my %profile;
%profile{$_} = [0 xx N] for <A C G T>;

for @default-data[] {
    my @dna = .comb;
    my %dna-index-map = classify { @dna[$_] }, ^@dna;
    for %dna-index-map.kv -> $k, $v {
        %profile{$k}[$v[]]»++;
    }
}
my @profile = %profile<A C G T>;

say my $consensus = [~] gather
for ^N -> \c {
    my $max = max map { @profile[$_][c] }, ^4;
    take <A C G T>[$_] given first { @profile[$_][c] == $max }, ^4;
}

say [~] .key, ': ', @profile[.value] for enum <A C G T>.sort;

# 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|#>
    =item2 L<empty|#>

=end nested
=begin nested :!nested

=item1 B<L<Documentation|/doc>>
    =item2 L<Getting started, Migration guides from other languages, & Tutorials | file:../doc/introduction.podlite>
    =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

=item1 B<Resoures>
    =item2 L<Download | file:../download/index.podlite>
    =item2 L<empty|#>
    =item2 L<empty|#>
    =item2 L<empty|#>
    =item2 L<empty|#>
    =item2 L<empty|#>
    =item2 L<empty|#>
    =item2 L<empty|#>

=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|#>
    =item2 L<empty|#>

=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