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| bl_next_start_codon(3) | FreeBSD Library Functions Manual | bl_next_start_codon(3) |
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.");
SEE ALSO
next_stop_codon(3)
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