# Bioinformatics/Subsequence

Bioinformatics/Subsequence 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.

Randomly generate a string of   200   DNA bases   (represented by   A,  C,  G,  and  T).

Write a routine to find all the positions of a randomly generated subsequence   (four letters).

## 11l

Translation of: Python
```UInt32 seed = 34
F nonrandom_choice(lst)
:seed = (1664525 * :seed + 1013904223) [&] FFFF'FFFF
R lst[Int(:seed >> 16) % lst.len]

F generate_sequence(Int n)
R ((0 .< n).map(_ -> nonrandom_choice([‘A’, ‘C’, ‘G’, ‘T’]))).join(‘’)

F positions(dnaSeq, subSeq)
[Int] r
V start = 0
L
V? pos = dnaSeq.find(subSeq, start)
I pos == N
L.break
r.append(pos)
start = pos + 1
R r

F dna_findall(String needle, haystack) -> N
V pp = positions(haystack, needle)
I pp.empty
print(‘No matches found’)
E
print(‘Found ’needle‘ at the following indices:’)
L(p) pp
print(p‘:’(p + needle.len))

V dna_seq = generate_sequence(200)
V sample_seq = generate_sequence(4)

V c = 1
L(i) dna_seq
I c % 20 != 0 {print(i, end' ‘’)} E print(i)
c++
print("\nSearch Sample: "sample_seq)

dna_findall(sample_seq, dna_seq)```
Output:
```GAAGTGCTCAAACCCTTTTT
CCTTGCCGTAGGTTGTGCTG
CCGCCGCACACCCGCAACAG
CTTTTAGGCATAAGTATACG
GACCGCGGACGGGGCGTAAC
GGTGAACATTTTGCTAAATT
GGCTCTAGGGATGAGCCCTA
TAGCGCTGGGGACTACGCCC
CGGTAAAGATCGAGGCGACT
CACCGATTGCGCTAGGGACA

Search Sample: CGTA
Found CGTA at the following indices:
26:30
94:98
```

## Action!

```DEFINE SEQLEN="200"
DEFINE SUBLEN="4"

PROC RandomSeq(CHAR ARRAY s BYTE len)
CHAR ARRAY letters="ACGT"
BYTE i

FOR i=1 TO len
DO
s(i)=letters(Rand(4)+1)
OD
s(0)=len
RETURN

PROC PrintSeq(CHAR ARRAY s)
BYTE i

FOR i=1 TO s(0)
DO
IF i MOD 20=1 THEN
IF i<10 THEN Put(32) FI
IF i<100 THEN Put(32) FI
PrintB(i)
Print(": ")
FI
Put(s(i))
IF i MOD 20=0 THEN
PutE()
FI
OD
RETURN

BYTE FUNC StartsWith(CHAR ARRAY s,prefix BYTE start)
BYTE i

FOR i=1 TO prefix(0)
DO
IF s(start+i-1)#prefix(i) THEN
RETURN (0)
FI
OD
RETURN (1)

PROC Main()
CHAR ARRAY seq(SEQLEN+1),sub(SUBLEN+1)
BYTE i,notfirst

RandomSeq(seq,SEQLEN)
RandomSeq(sub,SUBLEN)

PrintE("Search sequence:")
PrintSeq(seq)
PutE()
PrintF("Subsequence to find: %S%E%E",sub)

PrintE("Found subsequence at positions:")
notfirst=0
FOR i=1 TO SEQLEN-SUBLEN
DO
IF StartsWith(seq,sub,i) THEN
IF notfirst THEN
Print(", ")
FI
notfirst=1
PrintF("%I-%I",i,i+SUBLEN-1)
FI
OD
IF notfirst=0 THEN
FI
RETURN```
Output:
```Search sequence:
1: CGACTCAGGAAGGCCACGTG
21: GTAACTTCTTAGTTACCGTA
41: AGGCTAATAGCTAGCGCTGC
61: GTGACCAGGCATAGTAACCG
81: GCACGCACGTTCACCAAGGG
101: GTCCCGATGGGAGGCACGTT
121: ACTACTCCAAGAACTGTAGT
141: AAGTTACCGAAAAGTTCTCA
161: TCCTTGGGTAGTGAGTACTT
181: TGTGCTATGAAAAATAAGGA

Subsequence to find: ACGC

Found subsequence at positions:
83-86
```

```with Ada.Text_Io;

procedure Sub_Sequence is

type Nucleotide is (A, C, G, T);

function To_Character (N : Nucleotide) return Character
is (case N is
when A => 'A', when C => 'C',
when G => 'G', when T => 'T');

package Random_Nucleotide is new Ada.Numerics.Discrete_Random (Nucleotide);
use Random_Nucleotide;

package Position_Io is new Ada.Text_Io.Integer_Io (Natural);

procedure Put_Bases (Seq : String; Width : Positive) is
First : Natural := Seq'First;
begin
while First < Seq'Last loop
declare
Last : constant Natural :=
Natural'Min (First + Width - 1, Seq'Last);
begin
Position_Io.Put (First); Put ("..");
Position_Io.Put (Last);  Put (" ");
Put (Seq (First .. Last));
New_Line;
First := Last + 1;
end;
end loop;
end Put_Bases;

Gen       : Generator;
Sequence  : String (1 .. 405);
Substring : String (1 ..   4);
Pos       : Natural := 0;
begin
Position_Io.Default_Width := 3;

Reset (Gen);

Sequence  := (others => To_Character (Random (Gen)));
Substring := (others => To_Character (Random (Gen)));

Put_Line ("Search sequence:");
Put_Bases (Sequence, Width => 50);
New_Line;

Put ("Substring to search: ");
Put (Substring);
New_Line;

loop
Pos := Ada.Strings.Fixed.Index (Sequence, Substring, Pos + 1);
exit when Pos = 0;
Put ("Found at position: ");
Position_Io.Put (Pos); Put ("..");
Position_Io.Put (Pos + Substring'Length - 1);
New_Line;
end loop;
end Sub_Sequence;
```
Output:
```Search sequence:
1.. 50 CCTACGGAAAAGTGATAAGGACAGATACATAATCCTAAAACCCTGGAAAA
51..100 CTTGTCTCGCCAGAGTAGGGCTCGGCAGGGGGGGCAGTGTTTTAAAACGT
101..150 CAGAGAATAGGCTCTACCTTGTTAGACTGCGAGTACTGGAGCGTAGTTCC
151..200 TATATTGCAAGCTGCTACAGTAAGTATCAAAGTATGCCACACATCCTTCT
201..250 ACAACCGGATTGGTTGCCCAGTAGAAGGCTCGTAGTCACCGGACACGCTG
251..300 TTCTTAAGGTCGGTAAGCTATTACGTCCATGGGAGATTCTCAAGGGTGCG
301..350 TTAGCGGACCCCCGTTACGTCCACGTATCTTCCGTCCAACTACCCCCTAA
351..400 TGTCATTGACATCGCCCGAGTATTTAATTTATTTGAACGGCACCAATTTA
401..405 GAGCT

Substring to search: TATT
Found at position: 153..156
Found at position: 269..272
Found at position: 371..374
Found at position: 380..383```

## Arturo

```bases: [`A` `G` `C` `T`]
randSeq: join map 1..200 => [sample bases]
randSub: join map 1..4 => [sample bases]

idx: 0

print "Random sequence:"
print join.with:"\n" split.every: 20 randSeq
print ""

print "Looking for subsequence:"
print randSub
print ""

while [(size randSeq) > idx + 4][
if prefix? slice randSeq idx idx+4 randSub ->
print ["Found subsequence at position:" idx]
idx: idx + 1
]
```
Output:
```Random sequence:
CACGCGCGTTAACCCTGCAT
CTTTTCTCTAAGATGATGCG
CTACTCTGCCCGATTACTAT
GATGTCACCGGCGGTTCGGC
GACTGGCGCTGGCAGAAAGC
GCATGTCAAATTGCCCCAGT
GTGCAAGTCCAAGTATTAGT
GAGGTGCTCCGCTTCGTCCG
GGGTCGACTCGGTCCCACTT
CATTACATGTTGGTAATAGT

Looking for subsequence:
CGGT

Found subsequence at position: 71
Found subsequence at position: 169```

## Factor

Works with: Factor version 0.99 2021-02-05
```USING: accessors formatting grouping io kernel math
math.functions.integer-logs math.parser random regexp sequences ;

: new-dna ( n -- str ) [ "ACGT" random ] "" replicate-as ;

:: .dna ( seq n -- )
seq length integer-log10 1 + :> d seq n group
[ n * d pad write ": " write write nl ] each-index ;

: .match ( slice -- ) [ from>> ] [ to>> ] bi "%d..%d\n" printf ;

: .matches ( slices -- )
"Matches found at the following indices:" print
[ .match ] each ;

: .locate ( slices -- )
[ "No matches found." print ] [ .matches ] if-empty ;

: .biosub ( dna-size row-size -- )
[ new-dna dup ] [ .dna nl ] bi*
4 new-dna dup "Subsequence to locate: %s\n" printf
<regexp> all-matching-slices .locate ;

80 10 .biosub nl
600 39 .biosub nl
```
Output:
``` 0: ATTCAAGGAC
10: CACTATTAAC
20: CTGCATTGTG
30: AGAACTTGCA
40: GTGTACCGAG
50: AGCGAGTTTA
60: AAGCAACACA
70: TCTTTACCGA

Subsequence to locate: GTAG
No matches found.

0: GATCTCGTCATGGTCCATCCTAACATTTCGGTTGTGGGC
39: GCATCCCGATAGGCGAAGTTAAATCTACGTAGTCCTACG
78: TCACGACGGAACATGATTGCCCACCGAAGTCGTAGGCGA
117: GCTAAAGTCGGTACATACACGATCTGCTATATTCGTTCT
156: CCGACACACGACATGCAATCCGAGAAGCTCTCGAAGTGC
195: GGTCAGATCCTCAGACTCGAACAGAGGAGACCTTAACTG
234: ATACCCACAGTACTTCTCGCATAACCTAAGCACCTATGC
273: TTACACCATCGTCCTGATATTGAGTGAGTCTGGTCGGAG
312: ATATTATCTAGCACCCTCAAGCTCTGTGTGCCACACCAG
351: GATTCCACTTCGCGCTTGCCTAGAGAAAGTAGAGTAGGT
390: GGTGTCATTAGTACACTGTTTGCGATGCACCAACCAAAC
429: CCGACCGCCATGATGACTGCTTTTCGGCCAACGTCAGAT
468: TAAGAGTACTTTTAGTAGCACCGCAAGCCAGCCGGTTTA
507: GCAAGATCCTGCAGCCTCCACGTTATTTCAGGTCTCTAA
546: GCGTTCTTTCCATGGAAGTAGTCACCGCTCCCGTTGCCA
585: ATGGACACAGACGTT

Subsequence to locate: ATAT
Matches found at the following indices:
145..149
289..293
312..316
```

## Go

Translation of: Wren
```package main

import (
"fmt"
"math/rand"
"regexp"
"time"
)

const base = "ACGT"

func findDnaSubsequence(dnaSize, chunkSize int) {
dnaSeq := make([]byte, dnaSize)
for i := 0; i < dnaSize; i++ {
dnaSeq[i] = base[rand.Intn(4)]
}
dnaStr := string(dnaSeq)
dnaSubseq := make([]byte, 4)
for i := 0; i < 4; i++ {
dnaSubseq[i] = base[rand.Intn(4)]
}
dnaSubstr := string(dnaSubseq)
fmt.Println("DNA sequnence:")
for i := chunkSize; i <= len(dnaStr); i += chunkSize {
start := i - chunkSize
fmt.Printf("%3d..%3d: %s\n", start+1, i, dnaStr[start:i])
}
fmt.Println("\nSubsequence to locate:", dnaSubstr)
var r = regexp.MustCompile(dnaSubstr)
var matches = r.FindAllStringIndex(dnaStr, -1)
if len(matches) == 0 {
fmt.Println("No matches found.")
} else {
fmt.Println("Matches found at the following indices:")
for _, m := range matches {
fmt.Printf("%3d..%-3d\n", m[0]+1, m[1])
}
}
}

func main() {
rand.Seed(time.Now().UnixNano())
findDnaSubsequence(200, 20)
fmt.Println()
findDnaSubsequence(600, 40)
}
```
Output:

Sample run:

```DNA sequnence:
1.. 20: GTTGCCCACACGTCTTATTG
21.. 40: TAAAAATCACCGTGCAGCGA
41.. 60: GGTTAAAAATGGTAGGAAAA
61.. 80: TATCCTCAGCCAGCGGTGCC
81..100: GGCCAACAAAAGGGACGTTG
101..120: GATTAAAGTAGGTCTAGGTA
121..140: TCTCGTATCCGGTTGATCCG
141..160: GGATGGTGGACGATATTGGA
161..180: GACCGGAGTGTACATCGGTG
181..200: TTGTCGCTTGCAGCTACGGT

Subsequence to locate: AATA
Matches found at the following indices:
59..62

DNA sequnence:
1.. 40: GTACAGCCACTGTTAGTAGACGGATGCTATTGGGACGCAA
41.. 80: CACATCAGTACACTGCTTGTTCGTAATCGCGTACCCAGCG
81..120: CAAAAGGAGGGGAGGAACCTGCTCAGACTGTCGCTAAAAA
121..160: CGAGCACGTGTCCTTACGCAGTGATGGTAGCGGTCCACGA
161..200: CTTCCACTGGCATAAGGAGAATGTTTAGTAACGCCCCTCA
201..240: TAGGTGCAATTCTACAGGTTAAGGGACCGTGGGATGTTTC
241..280: TATAAAAGTTGAAGAGATTACTAATCCGTCCCGTGCGCGT
281..320: GCCGCAATTTAGCGCCCGTTCTTGAGTAAACATACATGCA
321..360: CGCTCTTGAGTTTTCTAAAACCTGATCAAAACGGTCGCCC
361..400: ACATGCAGGAGCGCCGCAGGGTTTCAGAGGTCAACCATCG
401..440: GCAGCACACGTGAACCCTCTGTACTGACCAGGGGCTTGCT
441..480: CCTTGGTAGGAGATGGTGGAGAATGCGTCGATGCACTGAA
481..520: GCAGACCGCTGATAGCATGTACGATGTTTACGGGTTGACG
521..560: ATAGCTTTGCTAGTGATCGAACATATGATGAAAAACGCTT
561..600: CCATTGATAGAGCATCTTAGGAGCTCAGTCCAGTGACCTC

Subsequence to locate: AGGT
Matches found at the following indices:
202..205
216..219
388..391
```

## jq

Works with: jq

Works with gojq, the Go implementation of jq

Neither jq nor gojq currently has any PRNG built-ins so one possibility is to use a jq-coded PRNG function such as can be found at https://rosettacode.org/wiki/Random_numbers#jq

In practice, it's usually more convenient to use a utility such as gshuf or jot to provide the source of randomness. Here we use `jot -r N MIN MAX` but a fourth argument can also be used to specify a seed. An alternative would be to use `gshuf` along the lines of:

```# For 200 pseudo-random integers in the range 0 to 3 inclusive:
gshuf -i 0-3 -r -n 200 --random-source=/dev/random
```

Note that the indices shown below are offsets (i.e., the index origin is taken to be 0).

```#!/bin/bash

jot -r 200 0 3 | jq -nr --slurpfile four <(jot -r 4 0 3) '

# input: an array of integers
def toDNA:
def base: . as \$in | "ACGT" | .[\$in : \$in+1];
map(base) | join("");

([inputs] | toDNA) as \$strand
| (\$four  | toDNA) as \$four
| "Strand of length \(\$strand|length):",
\$strand,
"Zero-based indices of \(\$four):",
(\$strand | indices(\$four) | join(" "))
'
```
Output:
```./bioinformatics-subsequence.sh
Strand of length 200:
TGGGCCCAAGCATTGCCACGTAGCTTTGTCAGTGGGCTTGTAAGGGACGAACACAAACTCACAGACCAGGAATTCTCGAGTTCCAGTCCCCCCACTTGTCGCTATTTAGTTAAGACGTTCAGTTTCGTTGCGAACTGTGTCCCCCAGGCTAACGTGATGGGTGTCAGGAATCAATGGCCAACTTTCAGTTAGACTTGACC
Zero-based indices of CAAC:
178

./bioinformatics-subsequence.sh
Strand of length 200:
TAAGACTGCAGGGTACGAAGAGTGGAAGATTGGCTCGTACTTGTCGACGTCGCGTGACATAATCTCTGTGCTCGCCTCGCAGTAAGGGACTAGGTCCCGTTCGAGCGCCCTGCTAGAAGGAGCATCCTACCATGCTCTGATGACATCCTGTCGGCATTAGAGTTTCTACGACATCTAAAGAGTACGATCGACTTCCCAGT
Zero-based indices of GACA:
55 141 169
```

## Julia

```DNArand(n, bases=['A', 'T', 'C', 'G']) = String(rand(bases, n))

DNAsearch(needle, haystack, lap=true) =  findall(needle, haystack, overlap=lap)

const rand_string = DNArand(200)
const subseq = DNArand(4)

println("Search sequence:\n\$rand_string\nfor substring \$subseq. Found at positions: ")
foreach(p -> print(rpad(p[2], 8), p[1] % 10 == 0 ? "\n" : ""), enumerate(DNAsearch(subseq, rand_string)))
```
Output:
```Search sequence:
CCGAAGCCAGGAGGACTGAGCGCTTGCGTCCCGAGTTCTGCGACGAGTCTCTTCATTATAAGGCCACTGATTGCGCTCATCATGAGTGCCAGAAGCACCGCTAAACATAAGTGTCCTTTCTTCCTGACGCACTTGAAGATTGTGACCATTTGTGCGGGTTGTGAGTTAGGGGCTCTCATTGTACACGATCTATAGTGTGC
for substring CGCT. Found at positions:
21:24   74:77   99:102
```

## Nim

```import random, sequtils, strutils

proc dnaSequence(n: Positive): string =
## Create a random DNA sequence of length "n".
newSeqWith(n, sample("ACGT")).join()

proc positions(dnaSeq, subSeq: string): seq[int] =
## Return the list of starting positions of a subsequence
## "subSeq" in a sequence "dnaSeq". Positions start at 1.
var start = 0
while true:
let pos = dnaSeq.find(subSeq, start)
if pos < 0: break
start = pos + 1

when isMainModule:

const
N = 200
Step = 20

randomize()

let dnaSeq = dnaSequence(N)
echo "DNA sequence:"
for i in countup(0, N - 1, Step):
echo (\$(i+1)).align(3), ' ', dnaSeq[i..i+(Step-1)]

let subSeq = dnaSequence(3)
echo "\nDNA subsequence: ", subSeq

echo()
let pos = dnaSeq.positions(subSeq)
if pos.len == 0:
else:
let tail = if pos.len == 1: ": " else: "s: "
echo "Subsequence found at position", tail, pos.join(", ")
```
Output:
```DNA sequence:
1 CACATACGATGAGCTGGGCG
21 CCTAAGAGGCGGAAAGACAA
41 CCGTGTGTGTCTAACCCATG
61 GTTTAATTGCAGATAGTCTC
81 TAGACTACAAACATTAGAGC
101 AATGCACCGGGGTGCACGTG
121 TGTTTTGACTTCCCATGAAA
141 GCCCTTATCCTAGAGTACAG
161 TCGGCAAATGTTCGCTCCTT
181 GGCCCACTCCATTTGGACGG

DNA subsequence: GTT

Subsequence found at positions: 61, 122, 170```

## Perl

```use strict;
use warnings;
use feature 'say';

my @bases = <A C G T>;
my \$basecnt = 160;

my(\$string,\$target);
\$string .= \$bases[ int rand @bases ] for 1 .. \$basecnt;
\$target .= \$bases[ int rand @bases ] for 1 .. 4;
say "Target: \$target";
say 'Matches at these positions:';
say ((\$string =~ s/.{1,40}\K/\n/gr) =~ s/(\$target)/ >\$1< /gr);
```
Output:
```Target: CCTG
Matches at these positions:
9
90
157
TTGCC >CCTG< CAAAGTTAATAAGTAAACAATTAAGTGAGTG
CTCTAGGGTAAGGTGAGGGCGGGAAGGGGAAAAATACCGA
TGCGAG >CCTG< TAGAGCCGGGCCTCAAATTAAACGAAAAAT
ATAAGTTTGCTTGGCACGCTGTACTACTTATCC >CCTG< ACT```

## Phix

Currently only searches for non-overlapped sequences, but it should be pretty obvious how to change that, in which case the next underline will simply partially overwrite the previous, so you'll get eg "<=<==>".

```with javascript_semantics

constant cheat = false

function grandna(integer len)
string dna = repeat(' ',len)
for i=1 to len do dna[i] = "ACGT"[rand(4)] end for
return dna
end function

procedure show(string dna, test, sequence idx)
idx = deep_copy(idx) & length(dna)+100 -- (add an otherwise unused sentinel)
sequence s = split(trim(join_by(split(join_by(dna,1,10,""),"\n"),1,5," ")),"\n")
integer ii = 1,         -- idx index
i = idx[ii],    -- current target
ux = 1,         -- underline index (1..4)
ldx = 1         -- line index (1, 51, 101, etc)
for si=1 to length(s) do
printf(1,"%3d: %s\n",{ldx,s[si]})
ldx += 50
if i and i<ldx then
string ul = repeat(' ',59)
while i and i<ldx do
integer up = i-ldx+51       -- underline pos (relative to ldx)
up += floor((up-1)/10)+5    -- (plus any needed spacing)
ul[up] = "<==>"[ux]
ux += 1
i += 1
if ux>4 then
ux = 1
ii += 1
i = idx[ii]
end if
end while
printf(1,"%s\n",ul)
end if
end for
if length(idx)>1 then
string p = iff(length(idx)>1?"s":""),
t = join(apply(idx[1..\$-1],sprint),", ")
printf(1,"%s occurs at location%s: %s\n",{test,p,t})
else
printf(1,"%s does not occur\n",{test})
end if
end procedure

string dna = grandna(200),
test = grandna(4)
constant cheats = iff(cheat?{9,13,49,60,64,68}:{})
for i=1 to length(cheats) do
dna[cheats[i]..cheats[i]+3] = test
end for
sequence idx = match_all(test,dna)
show(dna,test,idx)
```
Output:

with cheat enabled

```  1: GGAGATATCG ACCGACCGAA GTAAAGTCAA AGTCGTCCAA TCCACGGACG
<= =><==>                                   <=
51: ACTTCAGCAC GACCGACCGA CCTATTTAAG AGACCACACT TAAGGAATCC
=>       < ==><==><== >
101: ATGCGAAATA AAAATGGGCG AGTAGCCGTG GGGCGCTAAA GCACCCACCT
151: AGTTTTCGCC GAAGTACTAG ACCACCTTCG GATCGACAAA GCTTTCACCA
<==>
CGAC occurs at locations: 9, 13, 49, 60, 64, 68, 184
```

with cheat disabled

```  1: TGATTTAAAC CGTGGTGCAA TTTATAAACA CTGCGATATG CCTCCTGATG
51: GCATGGTATT CGACACCAAG ACGCTGGTGG GCACACTGGC TTTCAGAATA
101: GGAGTCACAA TCCCTCTATG ATGTCCTCTA GCGGGTGTGT GTTCAGTGCC
151: AGCGCTTACT TCCGGCGTGG CCGACTCTTT TTAAAGCGTA TAGCTGGGGT
GCTA does not occur
```

## Python

Works with: Python version 3.8
Library: regex
```
from random import choice
import regex as re
import time

def generate_sequence(n: int ) -> str:
return "".join([ choice(['A','C','G','T']) for _ in range(n) ])

def dna_findall(needle: str, haystack: str) -> None:

if sum(1 for _ in re.finditer(needle, haystack, overlapped=True)) == 0:
print("No matches found")
else:
print(f"Found {needle} at the following indices: ")
for match in re.finditer(needle, haystack, overlapped=True):
print(f"{match.start()}:{match.end()} ")

dna_seq = generate_sequence(200)
sample_seq = generate_sequence(4)

c = 1
for i in dna_seq:
print(i, end="") if c % 20 != 0 else print(f"{i}")
c += 1
print(f"\nSearch Sample: {sample_seq}")

dna_findall(sample_seq, dna_seq)
```
Output:
```TTGCCCCTGTACTGAGCCCA
TAAGCTTGCACTCAAGGTTT
TGCCCCCTCATATTATAACG
CATCCATTATACAAAACCGA
TACCCTTCCGCATATTATGA
AAAGTGGCGAAGTGCCTTGA
TTTGCATTCATAGTACAACG
GTGCAAAAGCATTGTATGTC
TCACATTTACATGGGAAATG
CCTAGTAGGTGCAAGACCTG

Search Sample: TACA
Found TACA at the following indices:
69:73
133:137
167:171
```

## Racket

```#lang racket

(define (rand-seq n)
(build-string n (lambda _ (string-ref "TGAC" (random 4)))))

(define (subsequence-indices full part)
(let ((part-length (string-length part)) (full-length (string-length full)))
(for/list ((i (- full-length part-length))
#:when (for/and ((p part) (f (in-string full i))) (eq? p f)))
(cons i (+ i part-length -1)))))

(define (report-sequence s (l 50))
(string-join (for/list ((i (in-range 0 (string-length s) l)))
(format "~a: ~a" (~a #:width 4 i)
(substring s i (min (string-length s) (+ i l)))))
"\n"))

(define (Bioinformatics/Subsequence (full (rand-seq 400)) (sub (rand-seq 4)))
(printf "Indices of ~a in~%~a~%~a~%"
sub (report-sequence full) (subsequence-indices full sub)))

(module+ main (for ((i 4)) (Bioinformatics/Subsequence)))
```
Output:
```Indices of TTAC in
0   : TTATCCTACCGCGTAAGTTCAATGCTCACCGCAGTTTGCTAACCGTTCCT
50  : AAATTCACTTCCTAAGGTATCTTTCGCTTAATTGATGCCGATTGAATTCC
100 : ACGGAGGGCGTAATTGTTTCGGACTTTAGACCTGACATAAGGGCACACTA
150 : GTCCTATTGAATTTGGTGCTATTCGGCGACCTACTAACCTTAGTCAGTGA
200 : AGAGCCATCTCAAAAGTACAGTCATCCTCAAGTGTTACATACGGCACCAT
250 : GACAGTGTATAAGCATGGAGGTTGGCCTATCGTCATATCGAGGCGGCGCC
300 : ATAGACCGGCCAGGTGATGAGATCGACTTTAATGTTGTTGCTTAGCTTGA
350 : CCTCTAGTTTGGATTAAGACGGTCATAGATAGATAGACCGTAAAGTATTC
((234 . 237))
Indices of GTAA in
0   : GTCAGTCCACGCAAGAATAGCAGTTGAGTGGACAATTTATGAGACGGAGA
50  : TAAGTAACCCGCTCCGAGATAAACGTCAGCCGGATTCCGCTGAGTCGGTC
100 : GCCTTCCAAGTGGCAGCTTGTTTGCATTGCTTACAGTGACTTGAACGATC
150 : ACCTACTCGAGGACTCTGCGGGTATTCCAGTTGCCTTGCACTCAGCGATG
200 : CACAAACTTTAAATTATCACAGAAAGAATGTGATTCGGGTGGTCACCCTT
250 : ATCGGTGAAACCAGTCCTTCCATGGGCATATTCTGCGTCGAAATGAGCCC
300 : GCTGTTTACGTTGTACGAACTGGGGACCTAAGGAAACGGGCCGTTCTTAG
350 : GTGATGTCAGCTGCAACGAACTACTGTTAACCTTCTCGATCTGTTGAAAA
((53 . 56))
Indices of AACG in
0   : TTTACAGTACGATTCCGAAGACACAAGAATGCGCCGGCTGTGGGTAGGGG
50  : CGACCCTGCGCGACCTATAAAAGGGGCGACTCAATTTTAGGCCCACCACG
100 : GACCCAGCCCTGTGCACAGAGCGGGGCATTTTTACCTCGCGTGCGCACCA
150 : ACTGCGATCTGCCTTGTCACATAATCCCACATACGAGTTGTATCTCTAAG
200 : AAGGGATGAGGCCAATTTAAATCCGGGTGCATTTCTCGGGGGGAGACACC
250 : AATGAGAGTGGGGCAAGGTGGCGTAGAGAGCTAATCGGGTTTTATGACCG
300 : CGGAAGACCTGGGATACGTCTGGGTGATAACTGAGGGCAGGTCAACGAAC
350 : CCTGATGCGTAGCCACGTCTCAGCTATCGGGCCTGTTTTCATAGTCCATG
((343 . 346))
Indices of CAGC in
0   : TGTGAACCACTATGACACGCTACACGCCTCAAGTTGGCCCCCATATAAGA
50  : ATATCCATCGGTTAATGTGTCTCGCGGCCGTTAGAACAAGCACTAAAGTT
100 : AGAGAAACCAACCATTGGACTAGATCAACATCAACGTCGCTGATAATAAA
150 : TGTATATCTGATGTGGCCGTTCATAAAATCGTTAACTACAGGTATCAACA
200 : TAGTCTCCCAACTTATATAATTGGTTAACTTAGGAGGAGCTTGCACAGCT
250 : CAGCTATATGCTATCTGGCCCTGGGCTTGGTAGGCATCACGTCGTTATGC
300 : TGCGAACATCTCAAAGACAAACGTTGATCCAGCCCCTAGAGAGGTCATTA
350 : GGCCTCGACCCAATTTAACCTCCCACTCCGTGGGTACAGCTTGAACCCCC
((245 . 248) (250 . 253) (329 . 332) (386 . 389))```

## Raku

Chances are actually pretty small that a random 4 codon string will show up at all in a random 200 codon sequence. Bump up the sequence size to get a reasonable chance of multiple matches.

```use String::Splice:ver<0.0.3>;

my \$line = 80;

my \$haystack = [~] <A C G T>.roll(\$line * 8);

say 'Needle: ' ~ my \$needle = [~] <A C G T>.roll(4);

my \$these = \$haystack ~~ m:g/<\$needle>/;

my @match = \$these.map: { .from, .pos }

printf "From: %3s to %3s\n", |\$_ for @match;

my \$disp = \$haystack.comb.batch(\$line)».join.join("\n");

for @match.reverse {
\$disp.=&splice(.[1] + .[1] div \$line, "\e[0m" );
\$disp.=&splice(.[0] + .[0] div \$line, "\e[31m");
}

say \$disp;
```
Output:

Show in custom div to better display highlighting.

Needle: TAGC
From: 159 to 163
From: 262 to 266
From: 315 to 319
From: 505 to 509
From: 632 to 636
CATATGTGACACTGACAGCTCGCGCGAAAATCCGTGTGACGGTCTGAACACTATACTATAGGCCCGGTCGGCATTTGTGG
CTCCCCAGTGGAGAGACCACTCGTCAATTGCTGACGACTTAACACAAATCGAGTCGCCCTTAGTGCCAGACGGGACTCCT
AGCAAAGGGCGGCACGTGGTGACTCCCAATATGTGAGCATGCCATCTAATTGATCTGGGGGGTTTCGCGGGAATACCTAG
GGGCGTTCTGTCCATGGATCTCTAGCCCTGCGAAGAGATACCCGCAGTGAGTTGCACGTGCAAAGAACTTGTAACTAGCG
TATTCTGTATCCGCCGCGCGATATGCTTCTGCGGGATGTACTTCTTGTGACTAAGACTTTGTTATCCAAATTGACCAATA
TTCAACGGTCGACTCTCCGAGGCAGTATCGGTACGCCGAAAAATGGTTACTTCGGCCATACGTAACCTCTCAAGTCACGA
TTACAGCCCACGGGGGCTTACAGCATAGCTCCAAAGACATTCCAATTGAGCTACAACGTGTTCAGTGCGGAGCAGTATCC
AGTACTCGACTGTTATGGTAAAAGGGCATCGTGATCGTTTATATTAATCATTGGGACAGGTGGTTAATGTCATAGCTTAG

## REXX

This REXX version allows the user to specify:

•   length of the (random) DNA data sequence     (default is 200).
•   length of the (random) DNA sequence             (default is four).
•   DNA proteins to be used in the sequence         (default is ACGT).
•   width of the output lines of (random DNA)         (default is 100).
•   often (if ever) to add a blank to the output       (default is every 10 proteins).
•   DNA proteins to be searched in the data         (the default is four unique random proteins).
•   the seed for the RANDOM function so runs can be repeated with the same data     (no default).
```/*REXX pgm gens random DNA (ACGT) sequence & finds positions of a random 4─protein seq. */
parse arg totLen rndLen basePr oWidth Bevery rndDNA seed .
if totLen=='' | totLen==","  then totLen=   200  /*Not specified?  Then use the default.*/
if rndLen=='' | rndLen==","  then rndLen=     4  /* "      "         "   "   "     "    */
if basePr=='' | basePr==","  then basePr= 'acgt' /* "      "         "   "   "     "    */
if oWidth=='' | oWidth==","  then oWidth=   100  /* "      "         "   "   "     "    */
if Bevery=='' | Bevery==","  then Bevery=    10  /* "      "         "   "   "     "    */
if rndDNA=='' | rndDNA==","  then rndDNA=  copies(., rndLen)    /*what we're looking for*/
if datatype(seed, 'W')  then call random ,,seed  /*used to generate repeatable random #s*/
call genRnd                                      /*gen  data field of random proteins.  */
call show                                        /*show   "    "    "    "      "       */
say '  base DNA proteins used: '  basePr
say 'random DNA proteins used: '  dna?
call findRnd
if @=='' then do;  say "the random DNA proteins weren't found.";  exit 4;  end
say 'the random DNA proteins were found in positions:'     strip(@)
exit 0                                           /*stick a fork in it,  we're all done. */
/*──────────────────────────────────────────────────────────────────────────────────────*/
commas: parse arg ?;  do jc=length(?)-3  to 1  by -3; ?=insert(',', ?, jc); end;  return ?
/*──────────────────────────────────────────────────────────────────────────────────────*/
findRnd: @=;           p=0                       /*@:  list of the found target proteins*/
do until p==0;    p= pos(dna?, \$\$, p+1);     if p>0  then @= @ commas(p)
/*Found one?  Append it to the "Found"s*/
end   /*p*/;             return
/*──────────────────────────────────────────────────────────────────────────────────────*/
genRnd: dna?=;        use= basePr;     upper use basePr rndDNA;       lenB= length(basePr)
do k=1  for rndLEN;      x= substr(rndDNA, k, 1)
if x==.  then  do;  ?= random(1, length(use) );         x= substr(use, ?, 1)
use= delstr(use, ?, 1)   /*elide so no protein repeats*/
end
dna?= dna? || x                              /*build a random protein seq.*/
end   /*k*/
return
/*──────────────────────────────────────────────────────────────────────────────────────*/
show: say " index │"center('DNA sequence of ' commas(totLen)  " proteins", oWidth+10)
say "───────┼"center(''                                            , oWidth+10, '─')
\$=; \$\$=;                 idx= 1               /*gen data field of random proteins.*/
do j=1  for totLen;   c= substr( basePr, random(1, lenB), 1)
\$\$= \$\$ || c                                       /*append a random protein.  */
if Bevery\==0  then if j//Bevery==0  then \$= \$' ' /*possibly add a blank.     */
if length( space(\$ || c, 0) )<oWidth  then do;   \$= \$  ||  c;   iterate;   end
say strip( right(idx, 7)'│' \$, 'T');  \$=          /*display line ──► terminal.*/
idx= idx + oWidth                                 /*bump the index number.    */
end   /*j*/
if \$\==''  then say right(idx, 7)"│" strip(\$, 'T')    /*show residual protein data*/
say "───────┴"center(''                                            , oWidth+10, '─')
say;                return
```
output   when using the default inputs:
``` index │                                                 DNA sequence of  200  proteins
───────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────
1│ TTTTTAGCG CGTTTTGTAG CGCTCTAAAA ACCGTAGCTA TATTTCTCGA AGTTTCACCC AGCTCTTTTG CCCCAGGGTT GCGCTAAGCC CAGCTTCGAG
101│ GGGGCACAG GTAAAATACT ACCGTCCGTG GAGGGGGATG AATTGACCCG ACATTTTTTG AAGCATAACT CGTGACTCAA TATTGCATGA TTACACCAGC
───────┴──────────────────────────────────────────────────────────────────────────────────────────────────────────────

base DNA proteins used:  ACGT
random DNA proteins used:  GCAT

the random DNA proteins were found in positions: 162 184
```
output   when using the inputs of:     1000   ,   ,   ,   ,   tttt
``` index │                                       DNA sequence of  1,000  proteins
───────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────
1│ GTGATTTTT AGCGCGTTTT GTAGCGCTCT AAAAACCGTA GCTATATTTC TCGAAGTTTC ACCCAGCTCT TTTGCCCCAG GGTTGCGCTA AGCCCAGCTT
101│ GAGGGGGGC ACAGGTAAAA TACTACCGTC CGTGGAGGGG GATGAATTGA CCCGACATTT TTTGAAGCAT AACTCGTGAC TCAATATTGC ATGATTACAC
201│ AGCTAGGTT AGTGTAAAAA CCCCCCTATC TTCCTGATCA ATGGCGAGTA AAACATGCAA CCAATTTGTG AGCGAGTACT GGAAATTATT GTTTACGGGA
301│ AGGCACATG CTACGCGCAA CAGATATCTT AGACTGACCC TTTTAGAGTC ATAAGCCCCT GTCGCCTACA TGCTACTAAT ACTCCAACTA GCGGCGCACC
401│ TCAACCGGA TCATGGCGCC AGGGAAAATG TGGCGTAGCG ACGTGCTCAT CGCTCGCCGG GGAGAGCCTT TCAGAATCTC GAATAAAACC TGGTAATGAC
501│ TCATCAATC GTAATGGTCG TCTGGGGCAA GAAGCCGATA TTATAGACTC AGGTCAGACG TGTGCACAAC GGCAGAATTT ATAGTAATTC GCGTGAACTA
601│ GTTTCGGGA TAGGCCTACG ACCAATCATA GGACATTCGA TGCACGGTGT AGAAACAGTT CTCTGATGTT ACTCGGGATA ACACTCGCAA TCCCCTAGGA
701│ ACCGTGAGC GTCGCTAGTA TCTGAGATAG TCGCGACTGC CCAGCGGTCT TTAAGTTCGC ACACTACGGG ACTCCTAGTT CGCCCATTCA TGGCTATTTT
801│ CCTATCAGT CCAATCCCAC GGGGAGGGCA CTCGCGCAAT TCATTCAAAG AGGGCCATTT GCCGATATAA GGTCCATCAT CGGGAGGAAT ATGACTCCTG
901│ TTAGTATTA GAGCAGCCTC GCTGCGTACT ACTGTCAGTG GCCCGTCAGG GAAGGCAAAA CGTTTTTCCT CTAGGAATCC GTCAATTGGA CTTCTAGACT
───────┴──────────────────────────────────────────────────────────────────────────────────────────────────────────────

base DNA proteins used:  ACGT
random DNA proteins used:  TTTT

the random DNA proteins were found in positions: 5 6 16 69 157 158 159 340 796 797 962 963
```

## Ring

```/*-----------------------------------
# Project : DNA subsequences
# Date    : 2021/03/23
# Author  : Gal Zsolt (~ CalmoSoft ~)
# Email   : <calmosoft@gmail.com>
-----------------------------------*/

//-----------------------------------------

start = 0
base = ["A","C","G","T"]
dnaList = []
dnaSeq = []
ColLine = list(21)

C_Spacing = 2

C_ButtonDnaStyle  = ' background-color: Red; border-radius: 8px;'
Button = newlist(10,20)
LayoutButtonRow = list(10)

//-----------------------------------------

app = new qApp
{
win = new qWidget() {
setWindowTitle('DNA subsequences')
setWinIcon(self,AppFile("white.jpg"))
setStyleSheet('background-color:White')
setgeometry(560,180,300,300)
//reSize(400,400)
winheight = 10
fontSize = 8 # + (winheight / 100)

LayoutButtonMain = new QVBoxLayout()
LayoutButtonMain.setSpacing(C_Spacing)
LayoutButtonMain.setContentsmargins(0,0,0,0)

LabelInd = new qLabel(win) { settext("    DNA subsequences start positions:")
setAlignment(Qt_AlignHCenter | Qt_AlignVCenter)
setStyleSheet("background-color:yellow") }

ButtonInd = new QPushButton(win) { setStyleSheet("background-color:yellow") }

LabelFind = new qLabel(win) { settext("    DNA subsequence to find:")
setStyleSheet("background-color:yellow") }

ButtonFind = new QPushButton(win)

DnaSearch = new QPushButton(win) { setclickevent("pstart()")
setStyleSheet("background-color:yellow")
settext("Find")
}

for Col = 1 to 21
ColLine[Col] = new qLabel(win) {
setmaximumheight(20)
setAlignment(Qt_AlignHCenter | Qt_AlignVCenter)
setStyleSheet("background-color:darkgray")
setText(string(Col-1))
}
next

LayoutInd = new QHBoxLayout() { setSpacing(C_Spacing) setContentsMargins(0,0,0,0) }

LayoutTitleRow = new QHBoxLayout() { setSpacing(C_Spacing) setContentsMargins(0,0,0,0) }

for Col = 1 to 21
next

RowLine = list(10)

for Row = 1 to 10
Letter = "" + Row*20
if Row*20 < 100
Letter = "  " + Row*20
ok
RowLine[Row] = new qLabel(win) { setFont(new qFont("Verdana",fontSize,40,0))
setAlignment(Qt_AlignHCenter | Qt_AlignVCenter)
setStyleSheet("background-color:darkgray")
setText(Letter)
}
next

for Row = 1 to 10
LayoutButtonRow[Row] = new QHBoxLayout()
{
setSpacing(C_Spacing)
setContentsmargins(0,0,0,0)
}

for Col = 1 to 20
Button[Row][Col] = new QPushButton(win) {
setmaximumwidth(20)
}
next

next

LayoutDataRow = new QHBoxLayout() { setSpacing(C_Spacing) setContentsMargins(0,0,0,0) }

setLayout(LayoutButtonMain)

pStart()
show()
}
exec()
}

//-----------------------------------------

func pStart()
start = start + 1

dnaList = []
for row = 1 to 10
for col = 1 to 20
Button[row][col].settext("")
next
next
for nr = 1 to 200
rnd = random(3)+1
baseStr = base[rnd]
row = ceil(nr/20)
col = nr%20
if col = 0
col = 20
ok
Button[row][col].settext(baseStr)
next

startDna()

//-----------------------------------------

func startDna()

strDna = list2str(dnaList)
strDna = substr(strDna,nl,"")

while true
strBase = ""
for n = 1 to 4
rnd = random(3)+1
strBase = strBase + base[rnd]
next
ind = substr(strDna,strBase)
if ind > 0
exit
ok
end

showDna(dnaList)

//-----------------------------------------

func showDna(dnaList)

if start > 1
see nl
for n = 1 to len(dnaSeq)
for m = 0 to 3
ind = dnaSeq[n] + m
row = ceil(ind/20)
col = ind%20
if col = 0
col = 20
ok
Button[row][col].setstylesheet(C_ButtonStyle)
next
next
ok

dnaSeq = []
strDna = list2str(dnaList)
strDna = substr(strDna,nl,"")

while true
strBase = ""
for n = 1 to 4
rnd = random(3)+1
strBase = strBase + base[rnd]
next
ind = substr(strDna,strBase)
if ind > 0
exit
ok
end

ButtonFind.setStyleSheet("background-color:yellow")
ButtonFind.settext(strBase)

for n = 1 to 196
flag = 1
for m = 0 to 3
if dnaList[n+m] != strBase[m+1]
flag = 0
exit
ok
next
if flag = 1
ok
next

temp = ""
ButtonInd.settext("")
for nr = 1 to len(dnaList)
ind = find(dnaSeq,nr)
if ind > 0
temp = temp + string(dnaSeq[ind]) + " "
ButtonInd.settext(temp)
for n = nr to nr + 3
row = ceil(n/20)
col = n%20
if col = 0
col = 20
ok
Button[row][col].setStyleSheet(C_ButtonDnaStyle)
Button[row][col].settext(dnaList[n])
next
ok
next

//-----------------------------------------```

Output:

## Wren

Library: Wren-pattern
Library: Wren-str
Library: Wren-fmt
```import "random" for Random
import "/pattern" for Pattern
import "/str" for Str
import "/fmt" for Fmt

var rand = Random.new()
var base = "ACGT"

var findDnaSubsequence = Fn.new { |dnaSize, chunkSize|
var dnaSeq = List.filled(dnaSize, null)
for (i in 0...dnaSize) dnaSeq[i] = base[rand.int(4)]
var dnaStr = dnaSeq.join()
var dnaSubseq = List.filled(4, null)
for (i in 0...4) dnaSubseq[i] = base[rand.int(4)]
var dnaSubstr = dnaSubseq.join()
System.print("DNA sequence:")
var i = chunkSize
for (chunk in Str.chunks(dnaStr, chunkSize)) {
Fmt.print("\$3d..\$3d: \$s", i - chunkSize + 1, i, chunk)
i = i + chunkSize
}
System.print("\nSubsequence to locate: %(dnaSubstr)")
var p = Pattern.new(dnaSubstr)
var matches = p.findAll(dnaStr)
if (matches.count == 0) {
System.print("No matches found.")
} else {
System.print("Matches found at the following indices:")
for (m in matches) {
Fmt.print("\$3d..\$3d", m.index + 1, m.index + 4)
}
}
}

findDnaSubsequence.call(200, 20)
System.print()
findDnaSubsequence.call(600, 40)
```
Output:
```DNA sequence:
1.. 20: TATGGGCGCATTATGACAAC
21.. 40: GGCTACTGAAACGAAAATTC
41.. 60: ATGCCTTCGGAGGCTAGACC
61.. 80: ACTCATACATGATTTACAGC
81..100: TAGTCAGTTGCGTCCGCCAT
101..120: CCCGCATAACTATGTATTAC
121..140: GAGCATGTTCTGGCAACCTT
141..160: TCAGTGACAGTTCCTCAGGC
161..180: GCGTTCGCGTTGAAGGCCTC
181..200: CCCACACCGCACCCCTGCCG

Subsequence to locate: AATT
Matches found at the following indices:
36.. 39

DNA sequence:
1.. 40: GCGCTGAGCGCCCCAGTACAGCGGGTTAAACCGAGCCCGC
41.. 80: TCCGATGAACCAACTCCCATTCCTATAATGGTGCCCCGAC
81..120: ATATTGAATTCGGCGGGTCCGCTATCGGGCTGAGGATGCC
121..160: AATATCTAGGCGCTACCCTGAAGATCCTCAGTTGTGGTGT
161..200: CGCGGAGTGTCGATCCCAGAGCTCCCAATTGACTCAATTA
201..240: CTTTTTCCGTCCTCTTGCTTACGGATTTATGTTTGTGGCA
241..280: GAGGTTATGCTTCAGGCATCCCCATGTTTCCTGAGATACG
281..320: ACCACTGTCAGGTGGCTTGAATCTACCTTGTATTTCCTCT
321..360: AGTACCAGTCACTGTCATCTACTGGAAGCCATATCAGCGT
361..400: TGAAATGTCTATAATTTACTCTCCGGTTGTACCCAAGCGA
401..440: TAACAGCAACGTGTGGGTCTAAAGAGTTCCGCGTTTCGAC
441..480: ATAACGTGCTCCTATTTATCTACCGAAACACCCTATTTTC
481..520: CATCTAACCGGCACCCAATGCGCAGGTGTACGCGTCCTAC
521..560: TACGTTTGAAACGGTTCCATCTCGCCATGTACAATTGTGG
561..600: GGCTACGATTAAGTGTAGTCGGTAATTCAGGGTGAAGTTG

Subsequence to locate: TTCG
Matches found at the following indices:
89.. 92
435..438
```