Bioinformatics/Global alignment

Bioinformatics/Global alignment is a draft programming task. It is not yet considered ready to be promoted as a complete task, for reasons that should be found in its talk page.

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.

Current DNA sequencers find the sequence for multiple small segments of DNA which have mostly randomly formed by splitting a much larger DNA molecule into shorter segments. When re-assembling such segments of DNA sequences into a larger sequence to form, for example, the DNA coding for the relevant gene, the overlaps between multiple shorter sequences are commonly used to decide how the longer sequence is to be assembled. For example, "AAGATGGA", GGAGCGCATC", and "ATCGCAATAAGGA" can be assembled into the sequence "AAGATGGAGCGCATCGCAATAAGGA" by noting that "GGA" is at the tail of the first string and head of the second string and "ATC" likewise is at the tail of the second and head of the third string.

When looking for the best global alignment in the output strings produced by DNA sequences, there are typically a large number of such overlaps among a large number of sequences. In such a case, the ordering that results in the shortest common superstring is generrally preferred.

Finding such a supersequence is an NP-hard problem, and many algorithms have been proposed to shorten calculations, especially when many very long sequences are matched.

The shortest common superstring as used in bioinfomatics here differs from the string task Shortest_common_supersequence. In that task, a supersequence may have other characters interposed as long as the characters of each subsequence appear in order, so that (abcbdab, abdcaba) -> abdcabdab. In this task, (abcbdab, abdcaba) -> abcbdabdcaba.

Task

•   Given N non-identical strings of characters A, C, G, and T representing N DNA sequences, find the shortest DNA sequence containing all N sequences.

•   Handle cases where two sequences are identical or one sequence is entirely contained in another.

•   Print the resulting sequence along with its size (its base count) and a count of each base in the sequence.

•   Find the shortest common superstring for the following four examples:

 

("TA", "AAG", "TA", "GAA", "TA")

("CATTAGGG", "ATTAG", "GGG", "TA")

("AAGAUGGA", "GGAGCGCAUC", "AUCGCAAUAAGGA")

("ATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTAT",
"GGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGT",
"CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA",
"TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC",
"AACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT",
"GCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTC",
"CGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCT",
"TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC",
"CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGC",
"GATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATT",
"TTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC",
"CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA",
"TCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGA")

Related tasks

• Bioinformatics base count.
• Bioinformatics sequence mutation.

Go

Translation of: Julia

<lang go>package main

import (

   "fmt"
   "strings"

)

/* Gets n! for small n. */ func factorial(n int) int {

   fact := 1
   for i := 2; i <= n; i++ {
       fact *= i
   }
   return fact

}

/* Gets all permutations of a list of strings. */ func getPerms(input []string) [][]string {

   perms := [][]string{input}
   le := len(input)
   a := make([]string, le)
   copy(a, input)
   n := le - 1
   fact := factorial(n + 1)

   for c := 1; c < fact; c++ {
       i := n - 1
       j := n
       for i >= 0 && a[i] > a[i+1] {
           i--
       }
       if i == -1 {
           i = n
       }
       for a[j] < a[i] {
           j--
       }
       a[i], a[j] = a[j], a[i]
       j = n
       i++
       if i == n+1 {
           i = 0
       }
       for i < j {
           a[i], a[j] = a[j], a[i]
           i++
           j--
       }
       b := make([]string, le)
       copy(b, a)
       perms = append(perms, b)
   }
   return perms

}

/* Returns all distinct elements from a list of strings. */ func distinct(slist []string) []string {

   distinctSet := make(map[string]int, len(slist))
   i := 0
   for _, s := range slist {
       if _, ok := distinctSet[s]; !ok {
           distinctSet[s] = i
           i++
       }
   }
   result := make([]string, len(distinctSet))
   for s, i := range distinctSet {
       result[i] = s
   }
   return result

}

/* Given a DNA sequence, report the sequence, length and base counts. */ func printCounts(seq string) {

   bases := [][]rune{{'A', 0}, {'C', 0}, {'G', 0}, {'T', 0}}
   for _, c := range seq {
       for _, base := range bases {
           if c == base[0] {
               base[1]++
           }
       }
   }
   sum := 0
   fmt.Println("\nNucleotide counts for", seq, "\b:\n")
   for _, base := range bases {
       fmt.Printf("%10c%12d\n", base[0], base[1])
       sum += int(base[1])
   }
   le := len(seq)
   fmt.Printf("%10s%12d\n", "Other", le-sum)
   fmt.Printf("  ____________________\n%14s%8d\n", "Total length", le)

}

/* Return the position in s1 of the start of overlap of tail of string s1 with head of string s2. */ func headTailOverlap(s1, s2 string) int {

   for start := 0; ; start++ {
       ix := strings.IndexByte(s1[start:], s2[0])
       if ix == -1 {
           return 0
       } else {
           start += ix
       }
       if strings.HasPrefix(s2, s1[start:]) {
           return len(s1) - start
       }
   }

}

/* Remove duplicates and strings contained within a larger string from a list of strings. */ func deduplicate(slist []string) []string {

   var filtered []string
   arr := distinct(slist)
   for i, s1 := range arr {
       withinLarger := false
       for j, s2 := range arr {
           if j != i && strings.Contains(s2, s1) {
               withinLarger = true
               break
           }
       }
       if !withinLarger {
           filtered = append(filtered, s1)
       }
   }
   return filtered

}

/* Returns shortest common superstring of a list of strings. */ func shortestCommonSuperstring(slist []string) string {

   ss := deduplicate(slist)
   shortestSuper := strings.Join(ss, "")
   for _, perm := range getPerms(ss) {
       sup := perm[0]
       for i := 0; i < len(ss)-1; i++ {
           overlapPos := headTailOverlap(perm[i], perm[i+1])
           sup += perm[i+1][overlapPos:]
       }
       if len(sup) < len(shortestSuper) {
           shortestSuper = sup
       }
   }
   return shortestSuper

}

func main() {

   testSequences := [][]string{
       {"TA", "AAG", "TA", "GAA", "TA"},
       {"CATTAGGG", "ATTAG", "GGG", "TA"},
       {"AAGAUGGA", "GGAGCGCAUC", "AUCGCAAUAAGGA"},
       {
           "ATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTAT",
           "GGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGT",
           "CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA",
           "TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC",
           "AACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT",
           "GCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTC",
           "CGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCT",
           "TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC",
           "CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGC",
           "GATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATT",
           "TTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC",
           "CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA",
           "TCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGA",
       },
   }

   for _, test := range testSequences {
       scs := shortestCommonSuperstring(test)
       printCounts(scs)
   }

}</lang>

Output:

Nucleotide counts for TAAGAA:

         A           4
         C           0
         G           1
         T           1
     Other           0
  ____________________
  Total length       6

Nucleotide counts for CATTAGGG:

         A           2
         C           1
         G           3
         T           2
     Other           0
  ____________________
  Total length       8

Nucleotide counts for AAGAUGGAGCGCAUCGCAAUAAGGA:

         A          10
         C           4
         G           8
         T           0
     Other           3
  ____________________
  Total length      25

Nucleotide counts for CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA:

         A          74
         C          57
         G          75
         T          94
     Other           0
  ____________________
  Total length     300

Julia

<lang julia>using Combinatorics

""" Given a DNA sequence, report the sequence, length and base counts""" function printcounts(seq)

   bases = [['A', 0], ['C', 0], ['G', 0], ['T', 0]]
   for c in seq, base in bases
       if c == base[1]
           base[2] += 1
       end
   end
   println("\nNucleotide counts for $seq:\n")
   for base in bases
       println(lpad(base[1], 10), lpad(string(base[2]), 12))
   end
   println(lpad("Other", 10), lpad(string(length(seq) - sum(x[2] for x in bases)), 12))
   println("     _________________\n", lpad("Total length", 14), lpad(string(length(seq)), 8))

end

"""Return the position in s1 of the start of overlap of tail of string s1 with head of string s2""" function headtailoverlap(s1, s2, minimumoverlap=1)

   start = 1
   while true
       range = findnext(s2[1:minimumoverlap], s1, start)
       range == nothing && return 0
       start = range.start
       startswith(s2, s1[start:end]) && return length(s1) - start + 1
       start += 1
   end

end

"""Remove duplicates and strings contained within a larger string from vector of strings""" function deduplicate(svect)

   filtered = empty(svect)
   arr = unique(svect)
   for (i, s1) in enumerate(arr)
       any(p -> p[1] != i && occursin(s1, p[2]), enumerate(arr)) && continue
       push!(filtered, s1)
   end
   return filtered

end

"""Returns shortest common superstring of a vector of strings""" function shortest_common_superstring(svect)

   ss = deduplicate(svect)
   shortestsuper = prod(ss)
   for perm in permutations(ss)
       sup = first(perm)
       for i in 1:length(ss)-1
           overlap_position = headtailoverlap(perm[i], perm[i+1], 1)
           sup *= perm[i + 1][overlap_position+1:end]
       end
       if length(sup) < length(shortestsuper)
           shortestsuper = sup
       end
   end
   return shortestsuper

end

testsequences = [ ["TA", "AAG", "TA", "GAA", "TA"], ["CATTAGGG", "ATTAG", "GGG", "TA"], ["AAGAUGGA", "GGAGCGCAUC", "AUCGCAAUAAGGA"], ["ATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTAT", "GGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGT", "CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA", "TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC", "AACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT", "GCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTC", "CGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCT", "TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC", "CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGC", "GATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATT", "TTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC", "CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA", "TCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGA"] ]

for test in testsequences

   scs = shortest_common_superstring(test)
   printcounts(scs)

end

</lang>

Output:

Nucleotide counts for TAAGAA:

         A           4
         C           0
         G           1
         T           1
     Other           0
     _________________
  Total length       6

Nucleotide counts for CATTAGGG:

         A           2
         C           1
         G           3
         T           2
     Other           0
     _________________
  Total length       8

Nucleotide counts for AAGAUGGAGCGCAUCGCAAUAAGGA:

         A          10
         C           4
         G           8
         T           0
     Other           3
     _________________
  Total length      25

Nucleotide counts for CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA:

         A          74
         C          57
         G          75
         T          94
     Other           0
     _________________
  Total length     300

Nim

Translation of: Wren

<lang Nim>import algorithm, sequtils, strformat, strutils, tables

const ACGT = ['A', 'C', 'G', 'T'] # Four DNA bases.

iterator permutations(slist: seq[string]): seq[string] =

 var slist = sorted(slist)
 yield slist
 while slist.nextPermutation():
   yield slist

proc printCounts(dnaSeq: string) =

 ## Given a DNA sequence, report the sequence, length and base counts.
 let counts = dnaSeq.toCountTable()
 echo &"\nNucleotide counts for {dnaSeq}:\n"
 for base in ACGT:
   echo &"{($base):>10} {counts[base]:11}"
 var others = 0
 for base in counts.keys:
   if base notin ACGT: inc others, counts[base]
 echo &"     Other {others:11}"
 echo &"  ————————————————————"
 echo &"  Total length {dnaSeq.len: 7}"

func headTailOverlap(s1, s2: string): int =

 ## Return the position in "s1" of the start of overlap
 ## of tail of string "s1" with head of string "s2".
 var start = 0
 while true:
   start = s1.find(s2[0], start)
   if start < 0: return 0
   if s2.startsWith(s1[start..^1]): return s1.len - start
   inc start

proc deduplicate(slist: seq[string]): seq[string] =

 ## Remove duplicates and strings contained within a larger string from a list of strings.
 let slist = sequtils.deduplicate(slist)
 for i, s1 in slist:
   block check:
     for j, s2 in slist:
       if j != i and s1 in s2:
         break check
     # "s1" is not contained in another string.
     result.add s1

func shortestCommonSuperstring(slist: seq[string]): string =

 ## Return shortest common superstring of a list of strings.

 let slist = slist.deduplicate()
 result = slist.join()
 for perm in slist.permutations():
   var sup = perm[0]
   for i in 0..<slist.high:
     let overlapPos = headTailOverlap(perm[i], perm[i+1])
     sup &= perm[i+1][overlapPos..^1]
   if sup.len < result.len: result = sup

const TestSequences = [

 @["TA", "AAG", "TA", "GAA", "TA"],
 @["CATTAGGG", "ATTAG", "GGG", "TA"],
 @["AAGAUGGA", "GGAGCGCAUC", "AUCGCAAUAAGGA"],
 @["ATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTAT",
   "GGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGT",
   "CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA",
   "TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC",
   "AACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT",
   "GCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTC",
   "CGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCT",
   "TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC",
   "CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGC",
   "GATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATT",
   "TTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC",
   "CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA",
   "TCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGA"]]

for test in TestSequences:

 let scs = test.shortestCommonSuperstring
 scs.printCounts()</lang>

Output:

Nucleotide counts for GAAGTA:

         A           3
         C           0
         G           2
         T           1
     Other           0
  ————————————————————
  Total length       6

Nucleotide counts for CATTAGGG:

         A           2
         C           1
         G           3
         T           2
     Other           0
  ————————————————————
  Total length       8

Nucleotide counts for AAGAUGGAGCGCAUCGCAAUAAGGA:

         A          10
         C           4
         G           8
         T           0
     Other           3
  ————————————————————
  Total length      25

Nucleotide counts for CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA:

         A          74
         C          57
         G          75
         T          94
     Other           0
  ————————————————————
  Total length     300

Perl

<lang perl>#!/usr/bin/perl

use strict; # https://rosettacode.org/wiki/Bioinformatics/global_alignment use warnings; use List::Util qw( first uniq );

my @seq = (

 [ qw( TA AAG TA GAA TA ) ],

 [ qw( CATTAGGG ATTAG GGG TA) ],

 [ qw( AAGAUGGA GGAGCGCAUC AUCGCAAUAAGGA ) ],

 [ qw(
 ATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTAT
 GGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGT
 CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
 TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC
 AACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
 GCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTC
 CGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCT
 TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC
 CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGC
 GATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATT
 TTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC
 CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
 TCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGA
 ) ],
 );

sub removedups # remove dups and subseqs

 {
 local $_ = join ' ', sort { length $a <=> length $b } split ' ', shift;
 1 while s/\b(\w+) (?=.*\1)//;
 return $_;
 }

for ( @seq )

 {
 local $_ = removedups join ' ', @$_;
 my @queue = $_;
 my @best;

 while( @queue )
   {
   local $_ = shift @queue;
   my @seq = split ' ', $_;
   my @over;
   for my $left ( @seq )
     {
     for my $right ( @seq )
       {
       $left eq $right and next;
       "$left $right" =~ /(.+) \1/ or next;
       my $len = length $1;
       $over[$len] .= "$left $right\n";
       }
     }
   if( @over )
     {
     for my $join ( split /\n/, $over[-1] )
       {
       my ($left, $right) = split ' ', $join;
       my @newseq = grep $_ ne $left && $_ ne $right, @seq; # remove used
       push @queue, removedups "$left $right" =~ s/(.+) (?=\1)//r .
         join ' ', , @newseq;
       }
     }
   else
     {
     tr/ //d;
     $best[length] .= "$_\n";
     next;
     }
   }

 for ( uniq split /\n/, first {defined} @best )
   {
   printf "\nlength %d - %s\n", length, $_;
   my %ch;
   $ch{$_}++ for /./g;
   use Data::Dump 'dd'; dd \%ch;
   }
 }</lang>

Output:

length 6 - TAGAAG
{ A => 3, G => 2, T => 1 }

length 8 - CATTAGGG
{ A => 2, C => 1, G => 3, T => 2 }

length 25 - AAGAUGGAGCGCAUCGCAAUAAGGA
{ A => 10, C => 4, G => 8, U => 3 }

length 300 - CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
{ A => 74, C => 57, G => 75, T => 94 }

Phix

procedure printcounts(sequence ss)
-- Given DNA sequence(s), report the sequence, length and base counts
    for i=1 to length(ss) do
        string dna = ss[i]
        sequence acgt = repeat(0,6)
        for j=1 to length(dna) do
            acgt[find(dna[j],"ACGT")+1] += 1
        end for
        acgt[$] = sum(acgt)
        string ncf = "Nucleotide counts for :"
        printf(1,"%s%s\n",{ncf,join(split_by(dna,50),"\n"&repeat(' ',length(ncf)))})
        printf(1,"Base counts: Other:%d, A:%d, C:%d, G:%d, T:%d, total:%d\n\n",acgt)
    end for
end procedure
 
function deduplicate(sequence ss)
-- Remove any strings contained within a larger string from a set of strings
    sequence filtered = {}
    for i=1 to length(ss) do
        string si = ss[i]
        bool found = false
        for j=1 to length(ss) do
            if i!=j and match(si,ss[j]) then
                found = true
                exit
            end if
        end for
        if not found then
            filtered = append(filtered, si)
        end if
    end for
    return filtered
end function
 
procedure shortest_common_superstring(sequence ss)
-- Returns shortest common superstring of a set of strings
    ss = deduplicate(unique(ss))
    sequence shortestsuper = {join(ss,"")}
    integer shortest = length(shortestsuper[1])
    for p=1 to factorial(length(ss)) do
        sequence perm = permute(p,ss)
        string sup = perm[1]
        for i=2 to length(perm) do
            string pi = perm[i]
            for j=-min(length(pi),length(sup)) to 0 do
                string overlap = sup[j..$]
                if overlap = pi[1..length(overlap)] then
                    sup &= pi[length(overlap)+1..$]
                    pi = ""
                    exit
                end if
            end for
            if length(pi) then ?9/0 end if -- (sanity chk)
        end for
        if length(sup) < shortest then
            shortest = length(sup)
            shortestsuper = {sup}
        elsif length(sup) = shortest
          and not find(sup,shortestsuper) then
            shortestsuper = append(shortestsuper,sup)
        end if
    end for
    printcounts(shortestsuper)
end procedure
 
constant tests = {
{"TA", "AAG", "TA", "GAA", "TA"},
{"CATTAGGG", "ATTAG", "GGG", "TA"},
{"AAGAUGGA", "GGAGCGCAUC", "AUCGCAAUAAGGA"},
{"ATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTAT",
"GGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGT",
"CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA",
"TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC",
"AACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT",
"GCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTC",
"CGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCT",
"TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC",
"CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGC",
"GATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATT",
"TTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC",
"CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA",
"TCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGA"}
}
papply(tests, shortest_common_superstring)

Output:

(Shows three length-6 results for the first test)

Nucleotide counts for :TAAGAA
Base counts: Other:0, A:4, C:0, G:1, T:1, total:6

Nucleotide counts for :GAAGTA
Base counts: Other:0, A:3, C:0, G:2, T:1, total:6

Nucleotide counts for :TAGAAG
Base counts: Other:0, A:3, C:0, G:2, T:1, total:6

Nucleotide counts for :CATTAGGG
Base counts: Other:0, A:2, C:1, G:3, T:2, total:8

Nucleotide counts for :AAGAUGGAGCGCAUCGCAAUAAGGA
Base counts: Other:3, A:10, C:4, G:8, T:0, total:25

Nucleotide counts for :CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
                       CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
                       AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
                       GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
                       CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
                       TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
Base counts: Other:0, A:74, C:57, G:75, T:94, total:300

Raku

Translation of: Go

Translation of: Julia

<lang perl6># 20210209 Raku programming solution

sub printCounts(\seq) {

  my $bases = seq.comb.Bag ;
  say "\nNucleotide counts for ", seq, " :";
  say $bases.kv, " and total length = ", $bases.total

}

sub stringCentipede(\s1, \s2) {

  loop ( my $offset = 0, my \S1 = $ =  ; ; $offset++ ) {
     S1 = s1.substr: $offset ;
     with S1.index(s2.substr(0,1)) -> $p { $offset += $p } else { return False }
     return s1.chars - $offset if s2.starts-with: s1.substr: $offset
  }

}

sub deduplicate {

  my @sorted = @_.unique.sort: *.chars; # by length   
  gather while ( my $target = shift @sorted ) {
     take $target unless @sorted.grep: { .contains: $target }  
  }

}

sub shortestCommonSuperstring {

  my \ß = $ = [~] my @ss = deduplicate @_ ;           # ShortestSuper
  for @ss.permutations -> @perm {
     my \sup = $ = @perm[0];
     for @perm.rotor(2 => -1) { sup ~= @_[1].substr: stringCentipede |@_ }
     ß = sup if sup.chars < ß.chars ;
  }
  ß

}

.&shortestCommonSuperstring.&printCounts for (

  <TA AAG TA GAA TA>,

  <CATTAGGG ATTAG GGG TA>,

  <AAGAUGGA GGAGCGCAUC AUCGCAAUAAGGA> ,

  <ATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTAT 
   GGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGT
   CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
   TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC
   AACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
   GCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTC
   CGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCT
   TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC
   CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGC
   GATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATT
   TTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC
   CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
   TCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGA
  >,

) </lang>

Output:

Nucleotide counts for TAAGAA :
(T 1 A 4 G 1) and total length = 6

Nucleotide counts for CATTAGGG :
(G 3 A 2 T 2 C 1) and total length = 8

Nucleotide counts for AAGAUGGAGCGCAUCGCAAUAAGGA :
(A 10 U 3 C 4 G 8) and total length = 25

Nucleotide counts for CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA :
(C 57 G 75 A 74 T 94) and total length = 300

Wren

Translation of: Julia

Library: Wren-fmt

Library: Wren-seq

Library: Wren-str

Library: Wren-math

<lang ecmascript>import "/fmt" for Fmt import "/seq" for Lst import "/str" for Str import "/math" for Int

/* Gets all permutations of a list of strings. */ var getPerms = Fn.new { |input|

   var perms = [input]
   var a = input.toList
   var n = a.count - 1
   for (c in 1...Int.factorial(n+1)) {
       var i = n - 1
       var j = n
       while (Str.gt(a[i], a[i+1])) i = i - 1
       while (Str.lt(a[j], a[i]))   j = j - 1
       var t = a[i]
       a[i] = a[j]
       a[j] = t
       j = n
       i = i + 1
       while (i < j) {
           t = a[i]
           a[i] = a[j]
           a[j] = t
           i = i + 1
           j = j - 1
       }
       perms.add(a.toList)
   }
   return perms

}

/* Given a DNA sequence, report the sequence, length and base counts. */ var printCounts = Fn.new { |seq|

   var bases = [["A", 0], ["C", 0], ["G", 0], ["T", 0]]
   for (c in seq) {
       for (base in bases) {
           if (c == base[0]) base[1] = base[1] + 1
       }
   }
   System.print("\nNucleotide counts for %(seq):\n")
   for (base in bases) Fmt.print("$10s$12d", base[0], base[1])
   var sum = bases.reduce(0) { |acc, x| acc + x[1] }
   Fmt.print("$10s$12d", "Other", seq.count - sum)
   Fmt.print("  ____________________\n$14s$8d", "Total length", seq.count)

}

/* Return the position in s1 of the start of overlap of tail of string s1 with head of string s2. */ var headTailOverlap = Fn.new { |s1, s2|

   var start = 0
   while (true) {
       start = s1.indexOf(s2[0], start)
       if (start == -1) return 0
       if (s2.startsWith(s1[start..-1])) return s1.count - start
       start = start + 1
   }

}

/* Remove duplicates and strings contained within a larger string from a list of strings. */ var deduplicate = Fn.new { |slist|

   var filtered = []
   var arr = Lst.distinct(slist)
   var i = 0
   for (s1 in arr) {
       var j = 0
       var withinLarger = false
       for (s2 in arr) {
           if (j != i && s2.contains(s1)) {
               withinLarger = true
               break
           }
           j = j + 1
       }
       if (!withinLarger) filtered.add(s1)
       i = i + 1
   }
   return filtered

}

/* Returns shortest common superstring of a list of strings. */ var shortestCommonSuperstring = Fn.new { |slist|

   var ss = deduplicate.call(slist)
   var shortestSuper = ss.join()
   for (perm in getPerms.call(ss)) {
       var sup = perm[0]
       for (i in 0...ss.count-1) {
           var overlapPos = headTailOverlap.call(perm[i], perm[i+1])
           sup = sup + perm[i+1][overlapPos..-1]
       }
       if (sup.count < shortestSuper.count) shortestSuper = sup
   }
   return shortestSuper

}

var testSequences = [

   ["TA", "AAG", "TA", "GAA", "TA"],
   ["CATTAGGG", "ATTAG", "GGG", "TA"],
   ["AAGAUGGA", "GGAGCGCAUC", "AUCGCAAUAAGGA"],
   [
       "ATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTAT",
       "GGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGT",
       "CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA",
       "TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC",
       "AACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT",
       "GCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTC",
       "CGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCT",
       "TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC",
       "CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGC",
       "GATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATT",
       "TTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC",
       "CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA",
       "TCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGA"
   ]

]

for (test in testSequences) {

   var scs = shortestCommonSuperstring.call(test)
   printCounts.call(scs)

}</lang>

Output:

Nucleotide counts for TAAGAA:

         A           4
         C           0
         G           1
         T           1
     Other           0
  ____________________
  Total length       6

Nucleotide counts for CATTAGGG:

         A           2
         C           1
         G           3
         T           2
     Other           0
  ____________________
  Total length       8

Nucleotide counts for AAGAUGGAGCGCAUCGCAAUAAGGA:

         A          10
         C           4
         G           8
         T           0
     Other           3
  ____________________
  Total length      25

Nucleotide counts for CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA:

         A          74
         C          57
         G          75
         T          94
     Other           0
  ____________________
  Total length     300