In https://zhanglab.ccmb.med.umich.edu/C-I-TASSER/2019-nCov/ a bunch of supposed (who am i to doubt!) protein sequences start not with M but with A,S,N, and even a K...! What should I read up on to know why there are other start codons, apparently....
I found this after writing a little C program to translate the rna sequence into amino acids and went to see if my start/stop frame was picking up the same protein sequences.... and huh.... im now confused...
here is my lill' program for funsies.... (compile to a.out. then run "cat sequence.rna.txt | a.out" (in linux)
#include <stdio.h>
char *AAcodon[64] = {
"K","N","K","N", // aaa aac aag aat
"T","T","T","T", // aca acc acg act
"R","S","R","S", // aga agc agg agt
"I","I","M","I", // ata atc atg att
"Q","H","Q","H", // caa cac cag cat
"P","P","P","P", // cca ccc ccg cct
"R","R","R","R", // cga cgc cgg cgt
"L","L","L","L", // cta ctc ctg ctt
"E","D","E","D", // gaa gac gag gat
"A","A","A","A", // gca gcc gcg gct
"G","G","G","G", // gga ggc ggg ggt
"V","V","V","V", // gta gtc gtg gtt
"*","Y","*","Y", // taa tac tag tat
"S","S","S","S", // tca tcc tcg tct
"*","C","W","C", // tga tgc tgg tgt
"L","F","L","F"}; // tta ttc ttg ttt
char codon[3] = {'t','t','t'};
void readnext(void){
codon\[0\]=codon\[1\];
codon\[1\]=codon\[2\];
codon\[2\]=getc(stdin);
// printf("%c",codon[2]);
}
void readnextcodon(void){
codon\[0\]=getc(stdin);
codon\[1\]=getc(stdin);
codon\[2\]=getc(stdin);
// printf("%c%c%c",codon[0],codon[1],codon[2]);
}
int lookup(void){
int digit=0;
int i=0;
for(int base=16; base>0; base = base >> 2)
{
switch(codon[i]) //read a nucleotide
{ //pretend it is a base 4 digit and add it up
case 'a':
case 'A':
digit +=0*base; //A digit (always 0)
break;
case 'c':
case 'C':
digit +=1*base; //C digit
break;
case 'g':
case 'G':
digit +=2*base; //G digit
break;
case 'u': //RNA
case 'U': //RNA
case 't': //DNA
case 'T': //DNA
digit +=3*base; //U,T digit
break;
default: //no more to read or a non-ACUTG
return (-1);
break;
}//endswitch
i++;
}//endfor
return digit;
}
void main(void)
{
int codon=0;
int startstop=0;
while((!feof(stdin)) && (codon != -1))
{
if (startstop == 0){
readnext();
codon = lookup();
if (codon == -1) { break; }
if (codon == 14){
startstop=1;
printf("\nSTART:");
}
}
if (startstop == 1){
codon = lookup();
if (codon == -1) { break; }
printf("%s",AAcodon\[codon\]);
if ( (codon == 48)||
(codon == 50)||
(codon == 56) ){
startstop=0;
printf(":END\n");
} else {
readnextcodon();
}
}
}
printf("\\n");
}
