/* Function: p7_prior_CreateLaplace()
* Synopsis: Creates Laplace plus-one prior.
* Incept: SRE, Sat Jun 30 09:48:13 2007 [Janelia]
*
* Purpose: Create a Laplace plus-one prior for alphabet <abc>.
*/
P7_PRIOR *
p7_prior_CreateLaplace(const ESL_ALPHABET *abc)
{
P7_PRIOR *pri = NULL;
int status;
ESL_ALLOC(pri, sizeof(P7_PRIOR));
pri->tm = pri->ti = pri->td = pri->em = pri->ei = NULL;
pri->tm = esl_mixdchlet_Create(1, 3); /* single component; 3 params */
pri->ti = esl_mixdchlet_Create(1, 2); /* single component; 2 params */
pri->td = esl_mixdchlet_Create(1, 2); /* single component; 2 params */
pri->em = esl_mixdchlet_Create(1, abc->K); /* single component; K params */
pri->ei = esl_mixdchlet_Create(1, abc->K); /* single component; K params */
if (pri->tm == NULL || pri->ti == NULL || pri->td == NULL || pri->em == NULL || pri->ei == NULL) goto ERROR;
pri->tm->pq[0] = 1.0; esl_vec_DSet(pri->tm->alpha[0], 3, 1.0); /* match transitions */
pri->ti->pq[0] = 1.0; esl_vec_DSet(pri->ti->alpha[0], 2, 1.0); /* insert transitions */
pri->td->pq[0] = 1.0; esl_vec_DSet(pri->td->alpha[0], 2, 1.0); /* delete transitions */
pri->em->pq[0] = 1.0; esl_vec_DSet(pri->em->alpha[0], abc->K, 1.0); /* match emissions */
pri->ei->pq[0] = 1.0; esl_vec_DSet(pri->ei->alpha[0], abc->K, 1.0); /* insert emissions */
return pri;
ERROR:
p7_prior_Destroy(pri);
return NULL;
}
/* Function: p7_prior_CreateAmino()
* Incept: SRE, Sat Mar 24 09:35:36 2007 [Janelia]
*
* Purpose: Creates the default mixture Dirichlet prior for protein
* sequences.
*
* The transition priors (match, insert, delete) are all
* single Dirichlets, originally trained by Graeme
* Mitchison in the mid-1990's. Notes have been lost, but
* we believe they were trained on an early version of
* Pfam.
*
* The match emission prior is a nine-component mixture
* from Kimmen Sjolander, who trained it on the Blocks9
* database \citep{Sjolander96}.
*
* The insert emission prior is a single Dirichlet with
* high $|\alpha|$, such that insert emission probabilities
* are essentially fixed by the prior, regardless of
* observed count data. The slightly polar parameterization
* was obtained by training on Pfam 1.0.
*
* Returns: a pointer to the new <P7_PRIOR> structure.
*/
P7_PRIOR *
p7_prior_CreateAmino(void)
{
int status;
P7_PRIOR *pri = NULL;
int q;
/* default match mixture coefficients: [Sjolander96] */
static double defmq[9] = {
0.178091, 0.056591, 0.0960191, 0.0781233, 0.0834977,
0.0904123, 0.114468, 0.0682132, 0.234585 };
/* default match mixture Dirichlet components [Sjolander96] */
static double defm[9][20] = {
{ 0.270671, 0.039848, 0.017576, 0.016415, 0.014268,
0.131916, 0.012391, 0.022599, 0.020358, 0.030727,
0.015315, 0.048298, 0.053803, 0.020662, 0.023612,
0.216147, 0.147226, 0.065438, 0.003758, 0.009621 },
{ 0.021465, 0.010300, 0.011741, 0.010883, 0.385651,
0.016416, 0.076196, 0.035329, 0.013921, 0.093517,
0.022034, 0.028593, 0.013086, 0.023011, 0.018866,
0.029156, 0.018153, 0.036100, 0.071770, 0.419641 },
{ 0.561459, 0.045448, 0.438366, 0.764167, 0.087364,
0.259114, 0.214940, 0.145928, 0.762204, 0.247320,
0.118662, 0.441564, 0.174822, 0.530840, 0.465529,
0.583402, 0.445586, 0.227050, 0.029510, 0.121090 },
{ 0.070143, 0.011140, 0.019479, 0.094657, 0.013162,
0.048038, 0.077000, 0.032939, 0.576639, 0.072293,
0.028240, 0.080372, 0.037661, 0.185037, 0.506783,
0.073732, 0.071587, 0.042532, 0.011254, 0.028723 },
{ 0.041103, 0.014794, 0.005610, 0.010216, 0.153602,
0.007797, 0.007175, 0.299635, 0.010849, 0.999446,
0.210189, 0.006127, 0.013021, 0.019798, 0.014509,
0.012049, 0.035799, 0.180085, 0.012744, 0.026466 },
{ 0.115607, 0.037381, 0.012414, 0.018179, 0.051778,
0.017255, 0.004911, 0.796882, 0.017074, 0.285858,
0.075811, 0.014548, 0.015092, 0.011382, 0.012696,
0.027535, 0.088333, 0.944340, 0.004373, 0.016741 },
{ 0.093461, 0.004737, 0.387252, 0.347841, 0.010822,
0.105877, 0.049776, 0.014963, 0.094276, 0.027761,
0.010040, 0.187869, 0.050018, 0.110039, 0.038668,
0.119471, 0.065802, 0.025430, 0.003215, 0.018742 },
{ 0.452171, 0.114613, 0.062460, 0.115702, 0.284246,
0.140204, 0.100358, 0.550230, 0.143995, 0.700649,
0.276580, 0.118569, 0.097470, 0.126673, 0.143634,
0.278983, 0.358482, 0.661750, 0.061533, 0.199373 },
{ 0.005193, 0.004039, 0.006722, 0.006121, 0.003468,
0.016931, 0.003647, 0.002184, 0.005019, 0.005990,
0.001473, 0.004158, 0.009055, 0.003630, 0.006583,
0.003172, 0.003690, 0.002967, 0.002772, 0.002686 },
};
ESL_ALLOC(pri, sizeof(P7_PRIOR));
pri->tm = pri->ti = pri->td = pri->em = pri->ei = NULL;
pri->tm = esl_mixdchlet_Create(1, 3); /* single component; 3 params */
pri->ti = esl_mixdchlet_Create(1, 2); /* single component; 2 params */
pri->td = esl_mixdchlet_Create(1, 2); /* single component; 2 params */
pri->em = esl_mixdchlet_Create(9, 20); /* 9 component; 20 params */
pri->ei = esl_mixdchlet_Create(1, 20); /* single component; 20 params */
if (pri->tm == NULL || pri->ti == NULL || pri->td == NULL || pri->em == NULL || pri->ei == NULL) goto ERROR;
/* Transition priors: originally from Graeme Mitchison. Notes are lost, but we believe
* they were trained on an early version of Pfam.
*/
pri->tm->pq[0] = 1.0;
pri->tm->alpha[0][0] = 0.7939; /* TMM */
pri->tm->alpha[0][1] = 0.0278; /* TMI */ /* Markus suggests ~10x MD, ~0.036; test! */
pri->tm->alpha[0][2] = 0.0135; /* TMD */ /* Markus suggests 0.1x MI, ~0.004; test! */
pri->ti->pq[0] = 1.0;
pri->ti->alpha[0][0] = 0.1551; /* TIM */
pri->ti->alpha[0][1] = 0.1331; /* TII */
pri->td->pq[0] = 1.0;
pri->td->alpha[0][0] = 0.9002; /* TDM */
pri->td->alpha[0][1] = 0.5630; /* TDD */
/* Match emission priors are from Kimmen Sjolander, trained
* on the Blocks9 database. [Sjolander96]
*/
for (q = 0; q < 9; q++)
{
pri->em->pq[q] = defmq[q];
esl_vec_DCopy(defm[q], 20, pri->em->alpha[q]);
}
/* Insert emission priors were trained on Pfam 1.0, 10 Nov 1996;
* see ~/projects/plan7/InsertStatistics.
* Inserts are slightly biased towards polar residues and away from
* hydrophobic residues.
*/
pri->ei->pq[0] = 1.0;
pri->ei->alpha[0][0] = 681.; /* A */
pri->ei->alpha[0][1] = 120.; /* C */
pri->ei->alpha[0][2] = 623.; /* D */
pri->ei->alpha[0][3] = 651.; /* E */
pri->ei->alpha[0][4] = 313.; /* F */
pri->ei->alpha[0][5] = 902.; /* G */
pri->ei->alpha[0][6] = 241.; /* H */
pri->ei->alpha[0][7] = 371.; /* I */
pri->ei->alpha[0][8] = 687.; /* K */
pri->ei->alpha[0][9] = 676.; /* L */
pri->ei->alpha[0][10] = 143.; /* M */
pri->ei->alpha[0][11] = 548.; /* N */
pri->ei->alpha[0][12] = 647.; /* P */
pri->ei->alpha[0][13] = 415.; /* Q */
pri->ei->alpha[0][14] = 551.; /* R */
pri->ei->alpha[0][15] = 926.; /* S */
pri->ei->alpha[0][16] = 623.; /* T */
pri->ei->alpha[0][17] = 505.; /* V */
pri->ei->alpha[0][18] = 102.; /* W */
pri->ei->alpha[0][19] = 269.; /* Y */
return pri;
ERROR:
if (pri != NULL) p7_prior_Destroy(pri);
return NULL;
}
/* Function: p7_prior_CreateNucleic()
*
* Purpose: Creates the default mixture Dirichlet prior for nucleotide
* sequences.
*
* The transition priors (match, insert, delete) are all
* single Dirichlets, trained on a portion of the rmark dataset
*
* The match emission prior is an eight-component mixture
* trained against a portion of the rmark dataset
*
* The insert emission prior is a single Dirichlet with
* high $|\alpha|$, such that insert emission probabilities
* are essentially fixed by the prior, regardless of
* observed count data.
*
* Returns: a pointer to the new <P7_PRIOR> structure.
*/
P7_PRIOR *
p7_prior_CreateNucleic(void)
{
int status;
P7_PRIOR *pri = NULL;
int q;
/* Plus-1 Laplace prior
int num_comp = 1;
static double defmq[2] = { 1.0 };
static double defm[1][4] = {
{ 1.0, 1.0, 1.0, 1.0} //
};
*/
/* Match emission priors are trained on Rmark3 database
* Xref: ~wheelert/notebook/2011/0325_nhmmer_new_parameters
*/
int num_comp = 4;
static double defmq[4] = { 0.24, 0.26, 0.08, 0.42 };
static double defm[4][4] = {
{ 0.16, 0.45, 0.12, 0.39},
{ 0.09, 0.03, 0.09, 0.04},
{ 1.29, 0.40, 6.58, 0.51},
{ 1.74, 1.49, 1.57, 1.95}
};
ESL_ALLOC(pri, sizeof(P7_PRIOR));
pri->tm = pri->ti = pri->td = pri->em = pri->ei = NULL;
pri->tm = esl_mixdchlet_Create(1, 3); // match transitions; single component; 3 params
pri->ti = esl_mixdchlet_Create(1, 2); // insert transitions; single component; 2 params
pri->td = esl_mixdchlet_Create(1, 2); // delete transitions; single component; 2 params
pri->em = esl_mixdchlet_Create(num_comp, 4); // match emissions; X component; 4 params
pri->ei = esl_mixdchlet_Create(1, 4); // insert emissions; single component; 4 params
if (pri->tm == NULL || pri->ti == NULL || pri->td == NULL || pri->em == NULL || pri->ei == NULL) goto ERROR;
/* Transition priors: roughly, learned from rmark benchmark - hand-beautified (trimming overspecified significant digits)
*/
pri->tm->pq[0] = 1.0;
pri->tm->alpha[0][0] = 2.0; // TMM
pri->tm->alpha[0][1] = 0.1; // TMI
pri->tm->alpha[0][2] = 0.1; // TMD
pri->ti->pq[0] = 1.0;
pri->ti->alpha[0][0] = 0.06; // TIM
pri->ti->alpha[0][1] = 0.2; // TII
pri->td->pq[0] = 1.0;
pri->td->alpha[0][0] = 0.1; // TDM
pri->td->alpha[0][1] = 0.2; // TDD
/* Match emission priors */
for (q = 0; q < num_comp; q++)
{
pri->em->pq[q] = defmq[q];
esl_vec_DCopy(defm[q], 4, pri->em->alpha[q]);
}
/* Insert emission priors. Should that alphas be lower? higher?
*/
pri->ei->pq[0] = 1.0;
esl_vec_DSet(pri->ei->alpha[0], 4, 1.0);
return pri;
ERROR:
if (pri != NULL) p7_prior_Destroy(pri);
return NULL;
}
/* Function: p7_prior_CreateNucleicNew()
* Incept: TJW, Thu Nov 12 21:15:11 EST 2009 [Couch at home]
*
* Purpose: Creates the default mixture Dirichlet prior for nucleotiden
* sequences.
*
* The transition priors (match, insert, delete) are all
* single Dirichlets, originally trained by Graeme
* Mitchison in the mid-1990's. Notes have been lost, but
* we believe they were trained on an early version of
* Pfam.
*
* The match emission prior is an eight-component mixture
* trained against a portion of the rmark dataset
*
* The insert emission prior is a single Dirichlet with
* high $|\alpha|$, such that insert emission probabilities
* are essentially fixed by the prior, regardless of
* observed count data.
*
* Returns: a pointer to the new <P7_PRIOR> structure.
*/
P7_PRIOR *
p7_prior_CreateNucleic(void)
{
int status;
P7_PRIOR *pri = NULL;
int q;
/* Match emission priors are trained on rmark database [Nawrocki 08]
*/
/* Plus-1 Laplace prior
int num_comp = 1;
static double defmq[2] = { 1.0 };
static double defm[1][4] = {
{ 1.0, 1.0, 1.0, 1.0} //
};
*/
/*
int num_comp = 2;
static double defmq[2] = { 0.42, 0.58 };
static double defm[2][4] = {
{ 0.94, 0.90, 0.89, 1.13}, //
{ 0.096, 0.078, 0.093, 0.089} //
};
*/
/*
//weird - but this performs marginally better than the best 2- 5- or 8-component mixtures tested
// (on rmark - MER: 2 better than 5/8-comp , 3 better than 2-comp )
int num_comp = 4;
static double defmq[4] = { 0.16, 0.29, 0.12, 0.43 };
static double defm[4][4] = {
{ 0.36, 0.10, 5.3, 0.13}, // G
{ 0.05, 0.18, 0.03, 0.19}, // CT
{ 7.1, 0.13, 0.35, 0.17}, // A
{ 0.96, 0.92, 0.91, 1.19} // uniform
};
*/
/*On rmark, this model does only slightly better than the 2-component model
It's chosen as the default on grounds of reasonableness, given that it shows
a non-uniform transition:transversion ratio. It's based on the results
of training against a portion of rmark, but the overspecified numbers
resulting from that training have been rounded/simplified.
*/
int num_comp = 5;
static double defmq[5] = { 0.16, 0.13, 0.17, 0.15, 0.39 };
static double defm[5][4] = {
{ 6.0, 0.2, 0.5, 0.2}, // A
{ 0.2, 8.0, 0.2, 0.5}, // C
{ 0.5, 0.2, 8.0, 0.2}, // G
{ 0.2, 0.5, 0.2, 4.0}, // T
{ 1.3, 1.2, 1.2, 1.4} // uniform
};
/* gives no improved performance in my hands over the 5-component model
int num_comp = 8;
static double defmq[8] = { 0.13, 0.08, 0.08, 0.13, 0.08, 0.08, 0.17, 0.25 } ;
static double defm[8][4] = {
{ 4.0, 0.3, 0.5, 0.4}, // A
{ 0.3, 22.0, 0.3, 0.8}, // C
{ 1.0, 0.4, 28.0, 0.4}, // G
{ 0.5, 0.8, 0.3, 6.0}, // T
{ 1.8, 0.8, 6.0, 1.0}, // AG
{ 0.6, 6.0, 0.6, 2.4}, // CT
{ 0.03, 0.01, 0.02, 0.02}, // anything, but highly conserved
{ 2.0, 2.0, 2.0, 2.0} // anything, not much conservation
};
*/
ESL_ALLOC(pri, sizeof(P7_PRIOR));
pri->tm = pri->ti = pri->td = pri->em = pri->ei = NULL;
pri->tm = esl_mixdchlet_Create(1, 3); // match transitions; single component; 3 params
pri->ti = esl_mixdchlet_Create(1, 2); // insert transitions; single component; 2 params
pri->td = esl_mixdchlet_Create(1, 2); // delete transitions; single component; 2 params
pri->em = esl_mixdchlet_Create(num_comp, 4); // match emissions; X component; 4 params
pri->ei = esl_mixdchlet_Create(1, 4); // insert emissions; single component; 4 params
if (pri->tm == NULL || pri->ti == NULL || pri->td == NULL || pri->em == NULL || pri->ei == NULL) goto ERROR;
/* Transition priors: roughly, learned from rmark benchmark - hand-beautified (trimming overspecified significant digits)
*/
pri->tm->pq[0] = 1.0;
pri->tm->alpha[0][0] = 2.0; // TMM
pri->tm->alpha[0][1] = 0.1; // TMI
pri->tm->alpha[0][2] = 0.1; // TMD
pri->ti->pq[0] = 1.0;
pri->ti->alpha[0][0] = 0.06; // TIM
pri->ti->alpha[0][1] = 0.2; // TII
pri->td->pq[0] = 1.0;
pri->td->alpha[0][0] = 0.1; // TDM
pri->td->alpha[0][1] = 0.2; // TDD
/* Match emission priors */
for (q = 0; q < num_comp; q++)
{
pri->em->pq[q] = defmq[q];
esl_vec_DCopy(defm[q], 4, pri->em->alpha[q]);
}
/* Insert emission priors. Should that alphas be lower? higher?
*/
pri->ei->pq[0] = 1.0;
esl_vec_DSet(pri->ei->alpha[0], 4, 1.0);
return pri;
ERROR:
if (pri != NULL) p7_prior_Destroy(pri);
return NULL;
}
