void embEstSetDebug (
void
);
| void: | No return value |
void embEstSetVerbose (
void
);
| void: | No return value |
ajint embEstGetSeed (
void
);
| ajint: | seed. |
void embEstMatInit (
ajint match,
ajint mismatch,
ajint gap,
ajint neutral,
char pad_char
);
| 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 |
| void: | No return value |
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
AjPSeq embEstFindSpliceSites (
const AjPSeq genome,
ajint forward
);
| genome: | (Input) | Genomic sequence |
| forward: | (Input) | Boolean. 1 = forward direction |
| AjPSeq: | Sequence of bitmask codes for splice sites. |
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
AjPSeq embEstShuffleSeq (
AjPSeq seq,
ajint in_place,
ajint* seed
);
| in_place: | (Input) | Boolean 1=shuffle in place |
| seq: | (Modify) | Original sequence |
| seed: | (Modify) | Random number seed. |
| AjPSeq: | shuffled sequence. |
void embEstFreeAlign (
EmbPEstAlign* ge
);
| ge: | (Delete) | Genomic EST alignment data structure |
| void: | No return value |
void embEstPrintAlign (
AjPFile ofile,
const AjPSeq genome,
const AjPSeq est,
const EmbPEstAlign ge,
ajint width
);
| genome: | (Input) | Genomic sequence |
| est: | (Input) | EST sequence |
| ge: | (Input) | Genomic EST alignment |
| width: | (Input) | Output width (in bases) |
| ofile: | (Modify) | Output file |
| void: | No return value |
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
EmbPEstAlign embEstAlignNonRecursive (
const AjPSeq est,
const AjPSeq genome,
ajint match,
ajint mismatch,
ajint gap_penalty,
ajint intron_penalty,
ajint splice_penalty,
const AjPSeq splice_sites,
ajint backtrack,
ajint needleman,
ajint init_path
);
| 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. |
| 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) |
| EmbPEstAlign: | Resulting genomic EST alignment |
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
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
);
| 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. |
| EmbPEstAlign: | Genomic EST alignment |
void embEstOutBlastStyle (
AjPFile blast,
const AjPSeq genome,
const AjPSeq est,
const EmbPEstAlign ge,
ajint match,
ajint mismatch,
ajint gap_penalty,
ajint intron_penalty,
ajint splice_penalty,
ajint gapped,
ajint reverse
);
| genome: | (Input) | Genomic sequence |
| est: | (Input) | EST sequence |
| ge: | (Input) | Genomic EST alignment |
| match: | (Input) | Match score |
| mismatch: | (Input) | Mismatch penalty |
| 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 |
| blast: | (Modify) | Output file |
| void: | No return value |