embest.c

Function embEstSetDebug

Prototype

void embEstSetDebug (
      void
);

Type	Name	Read/Write	Description
void		RETURN

From EMBOSS 1.13.0

Function embEstSetVerbose

Prototype

void embEstSetVerbose (
      void
);

Type	Name	Read/Write	Description
void		RETURN

From EMBOSS 1.13.0

Function embEstGetSeed

Prototype

ajint embEstGetSeed (
      void
);

Type	Name	Read/Write	Description
ajint		RETURN	seed.

From EMBOSS 1.13.0

Function embEstMatInit

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

From EMBOSS 1.13.0

Function embEstFindSpliceSites

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.

From EMBOSS 1.13.0

Function embEstShuffleSeq

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.

From EMBOSS 1.13.0

Function embEstFreeAlign

Prototype

void embEstFreeAlign (
      EmbPEstAlign* ge
);

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

From EMBOSS 1.13.0

Function embEstPrintAlign

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

From EMBOSS 1.13.0

Function embEstAlignNonRecursive

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

From EMBOSS 1.13.0

Function embEstAlignLinearSpace

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

From EMBOSS 1.13.0

Function embEstOutBlastStyle

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

From EMBOSS 1.13.0