NAME

bl_next_start_codon() - Find next start codon

LIBRARY

#include <biolibc/translate.h>
-lbiolibc

SYNOPSIS

long    bl_next_start_codon(FILE *rna_stream, char codon[4])

ARGUMENTS

rna_stream  FILE stream containing RNA sequence data
codon       4-character buffer to receive codon sequence
Set to "" if no codon found

DESCRIPTION

Locate the next start codon in stream and report its position in the input. Reported positions are 0-based offsets from the file position at the time of the call. Hence, to find the absolute positions of codons within a file stream across multiple calls to next_start_codon() or next_stop_codon(), their return values should added to the previous return value + 3 (the size of the previous codon). For example, givent the following input:

acaucauguucguggugacc

A call to next_start_codon() will return 5 (off set of AUG from the beginning of the sequence and a subsequent call to next_stop_codon() will return 7 (offset of UGA from the first base after the AUG).

RETURN VALUES

1-based position of the next start codon within the stream or EOF if no codon is found.

EXAMPLES

unsigned long   pos;
char            codon[4];
if ( (pos = next_start_codon(stdin)) != EOF )
{


    printf("Start codon at %lu.n", pos);


    if ( (pos = next_stop_codon(stdin, codon)) != EOF )


        printf("Stop codon %s at %lu.n", codon, pos);


    else


        puts("No stop codon found.");
}
else


    puts("No start codon found.");