A program to manipulate DNA and protein sequences. More...

#include "rwmolecule.h"
#include "rwgencode.h"
#include "seq_util.h"
#include "utilities.h"
#include "options.h"
#include "timer.h"

Functions
int	main (int argc, char **argv)

Variables
int	verbose

const char *	use []

Detailed Description

A program to manipulate DNA and protein sequences.

Author: Bernard Heymann

Date: Created: 20000808; Modified: 20190613

Function Documentation

◆ main()

int main	(	int	argc,
		char **	argv
	)

Variable Documentation

◆ use

const char* use[]

Initial value:

= {
" ",
"Usage: bseq [options] input.seq output.seq",
"------------------------------------------",
"Manipulates DNA and protein sequences.",
" ",
"Actions:",
"-show                    Show all DNA and protein sequences after other operations.",
"-Mass                    Show the calculated mass for each sequence.",
"-complement              Complement all DNA sequences before other operations.",
"-translate 1             Translate all DNA sequences with this frame (0,1,2).",
"-finddna ggattcga        DNA sequence to look for in DNA sequences.",
"-findprotein fghwereaas  Protein sequence to look for in protein sequences.",
"-findcoding aklsdrtv     Coding sequence to look for in DNA sequences.",
"                         Can be a file name with a protein sequence.",
" ",
"Parameters:",
"-verbose 7               Verbosity of output.",
"-nogaps                  Strip gaps from input sequences.",
"-length 1100,1500        Sequence length range to select for.",
"-number 10,14            Number of residues on either side to include in output.",
"-threshold 50            Threshold percentage to report hits (default only best hit).",
" ",
"Input:",
"-geneticcode file.star   Genetic code file (default = internal values).",
"-elements prop.star      Calculate elemental composition.",
" ",
NULL
}

◆ verbose

int verbose

extern