NumericAlign.c File Reference

Perform Needleman & Wunsch sequence alignment on two sequences encoded as numeric symbols. More...

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include "SysDefs.h"
#include "macros.h"
#include "array.h"
#include "general.h"
#include "seq.h"

Go to the source code of this file.

Data Structures
struct	XY

Macros
#define	DATAENV   "DATADIR" /* Environment variable or assign */
#define	MAXBUFF   2048

Functions
BOOL	blNumericReadMDM (char *mdmfile)
int	blNumericCalcMDMScore (int resa, int resb)
int	blNumericAffineAlign (int *seq1, int length1, int *seq2, int length2, BOOL verbose, BOOL identity, int penalty, int penext, int *align1, int *align2, int *align_len)

Detailed Description

Perform Needleman & Wunsch sequence alignment on two sequences encoded as numeric symbols.

Version

V1.3

Date

07.07.14

Copyright

(c) UCL / Dr. Andrew C. R. Martin / University of Reading 1993-2014

Author

Dr. Andrew C. R. Martin

Institute of Structural & Molecular Biology, University College London, Gower Street, London. WC1E 6BT.

andre.nosp@m.w@bi.nosp@m.oinf..nosp@m.org..nosp@m.uk andre.nosp@m.w.ma.nosp@m.rtin@.nosp@m.ucl..nosp@m.ac.uk

This code is NOT IN THE PUBLIC DOMAIN, but it may be copied according to the conditions laid out in the accompanying file COPYING.DOC.

The code may be modified as required, but any modifications must be documented so that the person responsible can be identified.

The code may not be sold commercially or included as part of a commercial product except as described in the file COPYING.DOC.

Note, the code herein is very heavily based on code written by Dr. Andrew C.R. Martin while self-employed. Some modifications were made to that original code while employed at University College London. This version which handles sequences encoded as arrays of numbers rather than as character arrays was modified from the original version(s) while employed at Reading University.

Description:

A simple Needleman & Wunsch Dynamic Programming alignment of 2 sequences encoded as numeric symbols. A window is not used so the routine may be a bit slow on long sequences.

Usage:

First call NumericReadMDM() to read the mutation data matrix, then call NumericAffineAlign() to align the sequences.

Revision History:

• V1.0 08.03.00 A modified version of align.c V2.12 written by ACRM from 19.06.90 to 06.03.00
• V1.1 28.09.00 Fixed bug at end of alignment if one sequence finishes first
• V1.2 06.02.03 Fixed for new version of GetWord()
• V1.3 07.07.14 Use bl prefix for functions By: CTP

Definition in file NumericAlign.c.

Macro Definition Documentation

#define DATAENV   "DATADIR" /* Environment variable or assign */

Definition at line 110 of file NumericAlign.c.

#define MAXBUFF   2048

Definition at line 112 of file NumericAlign.c.

Function Documentation

int blNumericAffineAlign	(	int *	seq1,
		int	length1,
		int *	seq2,
		int	length2,
		BOOL	verbose,
		BOOL	identity,
		int	penalty,
		int	penext,
		int *	align1,
		int *	align2,
		int *	align_len
	)

Parameters

[in]	*seq1	First sequence of tokens
[in]	length1	First sequence length
[in]	*seq2	Second sequence of tokens
[in]	length2	Second sequence length
[in]	verbose	Display N&W matrix
[in]	identity	Use identity matrix
[in]	penalty	Gap insertion penalty value
[in]	penext	Extension penalty
[out]	*align1	Sequence 1 aligned
[out]	*align2	Sequence 2 aligned
[out]	*align_len	Alignment length

Returns

Alignment score (0 on error)

Perform simple N&W alignment of seq1 and seq2. No window is used, so will be slow for long sequences.

The sequences come as integer arrays containing numeric tokens

Note that you must allocate sufficient memory for the aligned sequences. The easy way to do this is to ensure that align1 and align2 are of length (length1+length2).

Identical to align.c/affinealign(), but uses integer arrays

• 08.03.00 Original based on align.c/affinealign() 06.03.00 By: ACRM
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 412 of file NumericAlign.c.

int blNumericCalcMDMScore	(	int	resa,
		int	resb
	)

Parameters

[in]	resa	First token
[in]	resb	Second token

Returns

score

Calculate score from static globally stored mutation data matrix

Identical to align.c/CalcMDMScore(), but uses a different static score array and takes integer parameters. These are used as direct lookups into the score array rather than being searched.

• 08.03.00 Original based on align.c/CalcMDMScore() 11.07.96 By: ACRM
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 342 of file NumericAlign.c.

BOOL blNumericReadMDM

(

char *

mdmfile

)

Parameters

[in]

*mdmfile

Mutation data matrix filename

Returns

Success?

Read mutation data matrix into static global arrays. The matrix may have comments at the start introduced with a ! in the first column. The matrix must be complete (i.e. a triangular matrix will not work). A line describing the residue types must appear, and may be placed before or after the matrix itself

Identical to align.c/ReadMDM() but reads into a different static 2D array and doesn't read a symbol identifier line from the file as the symbols are numeric and always start from 1 (0 is used as the insert character)

• 08.03.00 Original based on align.c/ReadMDM() 26.07.95 By: ACRM
• 06.02.03 Fixed for new version of GetWord()
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 258 of file NumericAlign.c.