Bioinformatics/Global alignment
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
Go
<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
Phix
<lang 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)</lang>
- 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
<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.values.sum
}
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 0 }
S1 = s1.substr: $offset ;
return s1.chars - $offset if s2.starts-with: S1
}
}
sub deduplicate {
my @sorted = @_.unique.sort: { $^a.chars <=> $^b.chars } ; # by length
gather while ( my $target = shift @sorted ) {
take $target unless @sorted.grep: { .contains: $target }
}
}
sub shortestCommonSuperstring {
my @ss = deduplicate @_ ;
my \ß = $ = [~] @ss ; # ShortestSuper
for @ss.permutations -> @perm {
my \sup = $ = @perm[0];
for @perm.rotor(2 => -1) -> @duo {
my \overlapPos = stringCentipede @duo[0], @duo[1];
sup ~= @duo[1].substr: overlapPos;
}
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
<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