Bioinformatics/Subsequence: Difference between revisions

</pre>

=={{header|Action!}}==

<lang 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

PrintE("Not found")

FI

RETURN</lang>

{{out}}

[https://gitlab.com/amarok8bit/action-rosetta-code/-/raw/master/images/Bioinformatics_subsequence.png Screenshot from Atari 8-bit computer]

<pre>

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