Bioinformatics/Global alignment: Difference between revisions
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Automated syntax highlighting fixup (second round - minor fixes)
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[[Category:Strings]]
{{Draft task}}
Global alignment is designed to search for highly similar regions in two or more DNA sequences, where the
sequences appear in the same order and orientation, fitting the sequences in as pieces in a puzzle.
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:* [[Bioinformatics/Sequence_mutation|Bioinformatics sequence mutation]].
<br><br>
=={{header|11l}}==
{{trans|Nim}}
<syntaxhighlight lang="11l">-V ACGT = [‘A’, ‘C’, ‘G’, ‘T’]
F permutations(slist)
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Total length 300
</pre>
=={{header|Go}}==
{{trans|Julia}}
<syntaxhighlight lang="go">package main
import (
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Total length 300
</pre>
=={{header|jq}}==
{{works with|jq}}
'''Works with gojq, the Go implementation of jq'''
<syntaxhighlight lang="jq">
### Generic helper functions
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range(0;length) as $i
| [.[$i]] + (del(.[$i])|permutations)
end ;</syntaxhighlight><syntaxhighlight lang="jq">
# Give a synoptic view of the input string,
# highlighting the occurrence of ACGTU letters
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</syntaxhighlight>
'''The specific tasks'''
<syntaxhighlight lang="jq">
def examples:
[
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Σ: 300
</pre>
=={{header|Julia}}==
<syntaxhighlight lang="julia">using Combinatorics
""" Given a DNA sequence, report the sequence, length and base counts"""
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Total length 300
</pre>
=={{header|Nim}}==
{{trans|Wren}}
<syntaxhighlight lang=
const ACGT = ['A', 'C', 'G', 'T'] # Four DNA bases.
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————————————————————
Total length 300</pre>
=={{header|Pascal}}==
Used a matrix of head-tail overlapping and modified n-queens to generate the permutations.<BR>
Here nearly no runtime.But see [[N-queens_problem]] that using permutation is not the way for > 17<BR>
Of course this is more a traveling salesman problem.
<syntaxhighlight lang="pascal">
program BaseInDNA;
{$IFDEF FPC}
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A : 74 C : 57 G : 75 T : 94 U : 0
</pre>
=={{header|Perl}}==
<syntaxhighlight lang="perl">#!/usr/bin/perl
use strict; # https://rosettacode.org/wiki/Bioinformatics/global_alignment
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{ A => 74, C => 57, G => 75, T => 94 }
</pre>
=={{header|Phix}}==
<!--<syntaxhighlight lang=
<span style="color: #008080;">procedure</span> <span style="color: #000000;">printcounts</span><span style="color: #0000FF;">(</span><span style="color: #004080;">sequence</span> <span style="color: #000000;">ss</span><span style="color: #0000FF;">)</span>
<span style="color: #000080;font-style:italic;">-- Given DNA sequence(s), report the sequence, length and base counts</span>
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Base counts: Other:0, A:74, C:57, G:75, T:94, total:300
</pre>
=={{header|Python}}==
{{trans|Go}}
<syntaxhighlight lang="python">import os
from collections import Counter
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Total length 300
</pre>
=={{header|Raku}}==
{{trans|Go}}
{{trans|Julia}}
<syntaxhighlight lang="raku" line># 20210209 Raku programming solution
sub printCounts(\seq) {
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(C 57 G 75 A 74 T 94) and total length = 300
</pre>
=={{header|Wren}}==
{{trans|Julia}}
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{{libheader|Wren-str}}
{{libheader|Wren-math}}
<syntaxhighlight lang="ecmascript">import "/fmt" for Fmt
import "/seq" for Lst
import "/str" for Str
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