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.

Task

Genarate randomly a string (200 elements) of characters A, C, G, and T representing a DNA sequence write a routine to find the position of subsequence (also generating randomly).
Let length of subsequence equal to 4

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. <lang perl6>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;</lang>

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

Ring

<lang ring> row = 0 dnaList = [] base = ["A","C","G","T"] long = 20 see "DNA sequence:" + nl see " " + long + ": "

for nr = 1 to 200

   row = row + 1
   rnd = random(3)+1
   baseStr = base[rnd]
   see baseStr # + " "
   if (row%20) = 0 and long < 200
       long = long + 20
       see nl
       if long < 100
          see " " + long + ": "
       else
          see "" + long + ": "
       ok
   ok
   add(dnaList,baseStr)

next

strBase = "" for n = 1 to 4

   rnd = random(3)+1
   strBase = strBase + base[rnd]

next

see "subsequence to search: " + strBase + nl

seqok = 0

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
      seqok = 1
      see "start position of sequence = " + n + nl
   ok

next

if seqok = 0

  see "subsequence not found" + nl

ok </lang>

Output:

DNA sequence:
 20: GAGTATAAAAAGCGACATAG
 40: AAGCAGGGGGGGAACAGACA
 60: ACAATTGTGAAAACTAATCA
 80: ATACGGAAAAGGATAAACAT
100: GAGGGACTGCGGTTGGTAGG
120: CGATGAAACCTAAGAATGAA
140: AACGAGGAAGGTGTAAAGTG
160: ATGGGGTCATGGGACAGACA
180: TAGCTAAATGGATAAAAGCG
200: GGTGAAGTCGGTCGCAAACG
subsequence to search: ATGA
start position of subsequence = 79
start position of subsequence = 103
start position of subsequence = 116