embest.c

Synopsis

Prototype

void embEstSetDebug (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
void		RETURN

Returns

void:

No return value

Description

Sets debugging calls on

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Synopsis

Prototype

void embEstSetVerbose (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
void		RETURN

Returns

void:

No return value

Description

Sets verbose debugging calls on

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embEstGetSeed

Returns a seed for the random number generator, using the system clock.

Synopsis

Prototype

ajint embEstGetSeed (
      void
);

Type Name Read/Write Description

ajint RETURN seed.

Type	Name	Read/Write	Description
ajint		RETURN	seed.

Returns

ajint:

seed.

Description

Returns a seed for the random number generator, using the system clock.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Synopsis

Prototype

void embEstMatInit (
      ajint match,
      ajint mismatch,
      ajint gap,
      ajint neutral,
      char pad_char
);

Type Name Read/Write Description

ajint match Input Match code

ajint mismatch Input Mismatch penalty

ajint gap Input Gap penalty

ajint neutral Input Score for ambiguous base positions.

char pad_char Input Pad character for gaps in input sequences

void RETURN

Type	Name	Read/Write	Description
ajint	match	Input	Match code
ajint	mismatch	Input	Mismatch penalty
ajint	gap	Input	Gap penalty
ajint	neutral	Input	Score for ambiguous base positions.
char	pad_char	Input	Pad character for gaps in input sequences
void		RETURN

Input

match:	(Input)	Match code
mismatch:	(Input)	Mismatch penalty
gap:	(Input)	Gap penalty
neutral:	(Input)	Score for ambiguous base positions.
pad_char:	(Input)	Pad character for gaps in input sequences

Returns

void:

No return value

Description

Comparison matrix initialisation.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embEstFindSpliceSites

Finds all putative DONOR and ACCEPTOR splice sites in the genomic sequence.

Returns a sequence object whose "dna" should be interpreted as an array indicating what kind (if any) of splice site can be found at each sequence position.

DONOR sites are NNGTNN last position in exon

ACCEPTOR sites are NAGN last position in intron

if forward==1 then search fot GT/AG else search for CT/AC

Synopsis

Prototype

AjPSeq embEstFindSpliceSites (
      const AjPSeq genome,
      ajint forward 
);

Type Name Read/Write Description

const AjPSeq genome Input Genomic sequence

ajint forward Input Boolean. 1 = forward direction

AjPSeq RETURN Sequence of bitmask codes for splice sites.

Type	Name	Read/Write	Description
const AjPSeq	genome	Input	Genomic sequence
ajint	forward	Input	Boolean. 1 = forward direction
AjPSeq		RETURN	Sequence of bitmask codes for splice sites.

Input

genome:	(Input)	Genomic sequence
forward:	(Input)	Boolean. 1 = forward direction

Returns

AjPSeq:

Sequence of bitmask codes for splice sites.

Description

Finds all putative DONOR and ACCEPTOR splice sites in the genomic sequence.

Returns a sequence object whose "dna" should be interpreted as an array indicating what kind (if any) of splice site can be found at each sequence position.

DONOR sites are NNGTNN last position in exon

ACCEPTOR sites are NAGN last position in intron

if forward==1 then search fot GT/AG else search for CT/AC

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embEstShuffleSeq

Shuffle the sequence.

Synopsis

Prototype

AjPSeq embEstShuffleSeq (
      AjPSeq seq,
      ajint in_place,
      ajint* seed 
);

Type Name Read/Write Description

AjPSeq seq Modify Original sequence

ajint in_place Input Boolean 1=shuffle in place

ajint* seed Modify Random number seed.

AjPSeq RETURN shuffled sequence.

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Original sequence
ajint	in_place	Input	Boolean 1=shuffle in place
ajint*	seed	Modify	Random number seed.
AjPSeq		RETURN	shuffled sequence.

Input

in_place:

(Input)

Boolean 1=shuffle in place

Input & Output

seq:	(Modify)	Original sequence
seed:	(Modify)	Random number seed.

Returns

AjPSeq:

shuffled sequence.

Description

Shuffle the sequence.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embEstFreeAlign

Free a genomic EST alignment structure

Synopsis

Prototype

void embEstFreeAlign (
      EmbPEstAlign* ge
);

Type Name Read/Write Description

EmbPEstAlign* ge Delete Genomic EST alignment data structure

void RETURN

Type	Name	Read/Write	Description
EmbPEstAlign*	ge	Delete	Genomic EST alignment data structure
void		RETURN

Output

ge:

(Delete)

Genomic EST alignment data structure

Returns

void:

No return value

Description

Free a genomic EST alignment structure

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embEstPrintAlign

Print the alignment

Synopsis

Prototype

void embEstPrintAlign (
      AjPFile ofile,
      const AjPSeq genome,
      const AjPSeq est,
      const EmbPEstAlign ge,
      ajint width 
);

Type Name Read/Write Description

AjPFile ofile Modify Output file

const AjPSeq genome Input Genomic sequence

const AjPSeq est Input EST sequence

const EmbPEstAlign ge Input Genomic EST alignment

ajint width Input Output width (in bases)

void RETURN

Type	Name	Read/Write	Description
AjPFile	ofile	Modify	Output file
const AjPSeq	genome	Input	Genomic sequence
const AjPSeq	est	Input	EST sequence
const EmbPEstAlign	ge	Input	Genomic EST alignment
ajint	width	Input	Output width (in bases)
void		RETURN

Input

genome:	(Input)	Genomic sequence
est:	(Input)	EST sequence
ge:	(Input)	Genomic EST alignment
width:	(Input)	Output width (in bases)

Input & Output

ofile:

(Modify)

Output file

Returns

void:

No return value

Description

Print the alignment

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embEstAlignNonRecursive

Modified Smith-Waterman/Needleman to align an EST or mRNA to a Genomic sequence, allowing for introns.

The recursion is

{ S[gpos-1][epos] - gap_penalty

{ S[gpos-1][epos-1] + D[gpos][epos]

S[gpos][epos] = max { S[gpos][epos-1] - gap_penalty

{ C[epos] - intron_penalty

{ 0 (optional, only if ! needleman )

C[epos] = max{ S[gpos][epos], C[epos] }

S[gpos][epos] is the score of the best path to the cell gpos, epos C[epos] is the score of the best path to the column epos

Synopsis

Prototype

EmbPEstAlign embEstAlignNonRecursive (
      const AjPSeq est,
      const AjPSeq genome,
      ajint gap_penalty,
      ajint intron_penalty,
      ajint splice_penalty,
      const AjPSeq splice_sites,
      ajint backtrack,
      ajint needleman,
      ajint init_path
);

Type Name Read/Write Description

const AjPSeq est Input Sequence of EST

const AjPSeq genome Input Sequence of genomic region

ajint gap_penalty Input Gap penalty

ajint intron_penalty Input Intron penalty

ajint splice_penalty Input Splice site penalty

const AjPSeq splice_sites Input Marked splice sites. The intron_penalty may be modified to splice_penalty if splice_sites is non-null and there are DONOR and ACCEPTOR sites at the start and end of the intron.

ajint backtrack Input Boolean. If backtrack is 0 then only the start and end points and the score are computed, and no path matrix is allocated.

ajint needleman Input Boolean 1 = global alignment 0 = local alignment

ajint init_path Input Type of initialization for the path. If init_path is DIAGONAL then the boundary conditions are adjusted so that the optimal path enters the cell (0,0) diagonally. Otherwise it enters from the left (ie as a deletion in the EST)

EmbPEstAlign RETURN Resulting genomic EST alignment

Type	Name	Read/Write	Description
const AjPSeq	est	Input	Sequence of EST
const AjPSeq	genome	Input	Sequence of genomic region
ajint	gap_penalty	Input	Gap penalty
ajint	intron_penalty	Input	Intron penalty
ajint	splice_penalty	Input	Splice site penalty
const AjPSeq	splice_sites	Input	Marked splice sites. The intron_penalty may be modified to splice_penalty if splice_sites is non-null and there are DONOR and ACCEPTOR sites at the start and end of the intron.
ajint	backtrack	Input	Boolean. If backtrack is 0 then only the start and end points and the score are computed, and no path matrix is allocated.
ajint	needleman	Input	Boolean 1 = global alignment 0 = local alignment
ajint	init_path	Input	Type of initialization for the path. If init_path is DIAGONAL then the boundary conditions are adjusted so that the optimal path enters the cell (0,0) diagonally. Otherwise it enters from the left (ie as a deletion in the EST)
EmbPEstAlign		RETURN	Resulting genomic EST alignment

Input

est:	(Input)	Sequence of EST
genome:	(Input)	Sequence of genomic region
gap_penalty:	(Input)	Gap penalty
intron_penalty:	(Input)	Intron penalty
splice_penalty:	(Input)	Splice site penalty
splice_sites:	(Input)	Marked splice sites. The intron_penalty may be modified to splice_penalty if splice_sites is non-null and there are DONOR and ACCEPTOR sites at the start and end of the intron.
backtrack:	(Input)	Boolean. If backtrack is 0 then only the start and end points and the score are computed, and no path matrix is allocated.
needleman:	(Input)	Boolean 1 = global alignment 0 = local alignment
init_path:	(Input)	Type of initialization for the path. If init_path is DIAGONAL then the boundary conditions are adjusted so that the optimal path enters the cell (0,0) diagonally. Otherwise it enters from the left (ie as a deletion in the EST)

Returns

EmbPEstAlign:

Resulting genomic EST alignment

Description

Modified Smith-Waterman/Needleman to align an EST or mRNA to a Genomic sequence, allowing for introns.

The recursion is

{ S[gpos-1][epos] - gap_penalty

{ S[gpos-1][epos-1] + D[gpos][epos]

S[gpos][epos] = max { S[gpos][epos-1] - gap_penalty

{ C[epos] - intron_penalty

{ 0 (optional, only if ! needleman )

C[epos] = max{ S[gpos][epos], C[epos] }

S[gpos][epos] is the score of the best path to the cell gpos, epos C[epos] is the score of the best path to the column epos

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embEstAlignLinearSpace

Align EST sequence to genomic in linear space

Synopsis

Prototype

EmbPEstAlign embEstAlignLinearSpace (
      const AjPSeq est,
      const AjPSeq genome,
      ajint match,
      ajint mismatch,
      ajint gap_penalty,
      ajint intron_penalty,
      ajint splice_penalty,
      const AjPSeq splice_sites,
      float megabytes 
);

Type Name Read/Write Description

const AjPSeq est Input Sequence of EST

const AjPSeq genome Input Sequence of genomic region

ajint match Input Match score

ajint mismatch Input Mismatch penalty (positive)

ajint gap_penalty Input Gap penalty

ajint intron_penalty Input Intron penalty

ajint splice_penalty Input Splice site penalty

const AjPSeq splice_sites Input Marked splice sites. The intron_penalty may be modified to splice_penalty if splice_sites is non-null and there are DONOR and ACCEPTOR sites at the start and end of the intron.

float megabytes Input Maximum memory allowed in Mbytes for alignment by standard methods.

EmbPEstAlign RETURN Genomic EST alignment

Type	Name	Read/Write	Description
const AjPSeq	est	Input	Sequence of EST
const AjPSeq	genome	Input	Sequence of genomic region
ajint	match	Input	Match score
ajint	mismatch	Input	Mismatch penalty (positive)
ajint	gap_penalty	Input	Gap penalty
ajint	intron_penalty	Input	Intron penalty
ajint	splice_penalty	Input	Splice site penalty
const AjPSeq	splice_sites	Input	Marked splice sites. The intron_penalty may be modified to splice_penalty if splice_sites is non-null and there are DONOR and ACCEPTOR sites at the start and end of the intron.
float	megabytes	Input	Maximum memory allowed in Mbytes for alignment by standard methods.
EmbPEstAlign		RETURN	Genomic EST alignment

Input

est:	(Input)	Sequence of EST
genome:	(Input)	Sequence of genomic region
match:	(Input)	Match score
mismatch:	(Input)	Mismatch penalty (positive)
gap_penalty:	(Input)	Gap penalty
intron_penalty:	(Input)	Intron penalty
splice_penalty:	(Input)	Splice site penalty
splice_sites:	(Input)	Marked splice sites. The intron_penalty may be modified to splice_penalty if splice_sites is non-null and there are DONOR and ACCEPTOR sites at the start and end of the intron.
megabytes:	(Input)	Maximum memory allowed in Mbytes for alignment by standard methods.

Returns

EmbPEstAlign:

Genomic EST alignment

Description

Align EST sequence to genomic in linear space

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embEstOutBlastStyle

output in blast style.

Synopsis

Prototype

void embEstOutBlastStyle (
      AjPFile blast,
      const AjPSeq genome,
      const AjPSeq est,
      const EmbPEstAlign ge,
      ajint gap_penalty,
      ajint intron_penalty,
      ajint splice_penalty,
      ajint gapped,
      ajint reverse
);

Type Name Read/Write Description

AjPFile blast Modify Output file

const AjPSeq genome Input Genomic sequence

const AjPSeq est Input EST sequence

const EmbPEstAlign ge Input Genomic EST alignment

ajint gap_penalty Input Gap penalty

ajint intron_penalty Input Intron penalty

ajint splice_penalty Input Splice site penalty

ajint gapped Input Boolean. 1 = write a gapped alignment

ajint reverse Input Boolean. 1 = reverse alignment

void RETURN

Type	Name	Read/Write	Description
AjPFile	blast	Modify	Output file
const AjPSeq	genome	Input	Genomic sequence
const AjPSeq	est	Input	EST sequence
const EmbPEstAlign	ge	Input	Genomic EST alignment
ajint	gap_penalty	Input	Gap penalty
ajint	intron_penalty	Input	Intron penalty
ajint	splice_penalty	Input	Splice site penalty
ajint	gapped	Input	Boolean. 1 = write a gapped alignment
ajint	reverse	Input	Boolean. 1 = reverse alignment
void		RETURN

Input

genome:	(Input)	Genomic sequence
est:	(Input)	EST sequence
ge:	(Input)	Genomic EST alignment
gap_penalty:	(Input)	Gap penalty
intron_penalty:	(Input)	Intron penalty
splice_penalty:	(Input)	Splice site penalty
gapped:	(Input)	Boolean. 1 = write a gapped alignment
reverse:	(Input)	Boolean. 1 = reverse alignment

Input & Output

blast:

(Modify)

Output file

Returns

void:

No return value

Description

output in blast style.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

embest.c

Synopsis

Prototype

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input

Returns

Description

Usage

Example

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Availability

Synopsis

Prototype

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input

Input & Output