all posible sequences from consensus

Question

[hgarza]

Hi, this is my first post,

i have a consensus sequence: YYRNYY, where: Y = (C/T); R = (A/G); N = (A/C/G/T)

i want to obtain all possible combinations of nucleotides from the consensus sequence and add each one to a list and print it.

thanks

[GenoMax]

https://stackoverflow.com/questions/27551921/how-to-extend-ambiguous-dna-sequence

Answer 1

[Pierre Lindenbaum]

In C:

	/** compilation gcc -o biostars282490 biostars282490.c */
	#include <stdio.h>
	#include <stdlib.h>
	#include <string.h>
	#include <ctype.h>
	static void recursive(
	const char* src,
	char* dna,
	const int pos,
	const int len)
	{
	unsigned int i=0UL;
	char bases[5];
	if(pos==len)
	{
	fputs(dna,stdout);
	fputc('\n',stdout);
	return;
	}
	memset((void*)bases,0,5);
	switch (toupper(src[pos])) {
	case 'A':
	case 'C':
	case 'G':
	case 'T':
	case 'U':
	bases[0] = dna[pos];
	break;
	case 'R': bases[0] = 'A'; bases[1] = 'G'; break;
	case 'Y': bases[0] = 'C'; bases[1] = 'T'; break;
	case 'S': bases[0] = 'G'; bases[1] = 'C';break;
	case 'W': bases[0] = 'A'; bases[1] = 'T';break;
	case 'K': bases[0] = 'G'; bases[1] = 'T';break;
	case 'M': bases[0] = 'A'; bases[1] = 'C';break;
	case 'B': bases[0] = 'C'; bases[1] = 'G'; bases[2] = 'T'; break;
	case 'D': bases[0] = 'A'; bases[1] = 'G'; bases[2] = 'T'; break;
	case 'H': bases[0] = 'A'; bases[1] = 'C'; bases[2] = 'T'; break;
	case 'V': bases[0] = 'A'; bases[1] = 'C'; bases[2] = 'G'; break;
	case 'N': bases[0] = 'A'; bases[1] = 'C'; bases[2] = 'G'; bases[3] = 'T';break;
	}
	while(bases[i]!=0)
	{
	dna[pos]=bases[i++];
	recursive(src,dna,pos+1,len);
	}
	}
	int main(int argc,char** argv)
	{
	size_t len;
	char* src;
	char* dna;
	if(argc!=2)
	{
	fprintf(stderr,"Usage %s DNA\n",argv[0]);
	return EXIT_FAILURE;
	}
	src = argv[1];
	len = strlen(src);
	if(len==0UL)
	{
	fprintf(stderr,"Bad DNA\n");
	return EXIT_FAILURE;
	}
	dna=(char*)malloc(sizeof(char)*(len+1));
	if(dna==0)
	{
	fprintf(stderr,"Out of memory\n");
	return EXIT_FAILURE;
	}
	strcpy(dna,src);
	recursive(src,dna,0,len);
	free(dna);
	return EXIT_SUCCESS;
	}

view raw biostars282490.c hosted with ❤ by GitHub

./biostars282490 YYRNYY

CCAACC
CCAACT
CCAATC
CCAATT
CCACCC
CCACCT
CCACTC
CCACTT
CCAGCC
CCAGCT
CCAGTC
CCAGTT
CCATCC
CCATCT
CCATTC
CCATTT
CCGACC
CCGACT
CCGATC
CCGATT
CCGCCC
CCGCCT
CCGCTC
CCGCTT
CCGGCC
CCGGCT
CCGGTC
CCGGTT
CCGTCC
CCGTCT
CCGTTC
CCGTTT
CTAACC
CTAACT
CTAATC
CTAATT
CTACCC
CTACCT
CTACTC
CTACTT
CTAGCC
CTAGCT
CTAGTC
CTAGTT
CTATCC
CTATCT
CTATTC
CTATTT
CTGACC
CTGACT
CTGATC
CTGATT
CTGCCC
CTGCCT
CTGCTC
CTGCTT
CTGGCC
CTGGCT
CTGGTC
CTGGTT
CTGTCC
CTGTCT
CTGTTC
CTGTTT
TCAACC
TCAACT
TCAATC
TCAATT
TCACCC
TCACCT
TCACTC
TCACTT
TCAGCC
TCAGCT
TCAGTC
TCAGTT
TCATCC
TCATCT
TCATTC
TCATTT
TCGACC
TCGACT
TCGATC
TCGATT
TCGCCC
TCGCCT
TCGCTC
TCGCTT
TCGGCC
TCGGCT
TCGGTC
TCGGTT
TCGTCC
TCGTCT
TCGTTC
TCGTTT
TTAACC
TTAACT
TTAATC
TTAATT
TTACCC
TTACCT
TTACTC
TTACTT
TTAGCC
TTAGCT
TTAGTC
TTAGTT
TTATCC
TTATCT
TTATTC
TTATTT
TTGACC
TTGACT
TTGATC
TTGATT
TTGCCC
TTGCCT
TTGCTC
TTGCTT
TTGGCC
TTGGCT
TTGGTC
TTGGTT
TTGTCC
TTGTCT
TTGTTC
TTGTTT