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esl_composition.c
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/
esl_composition.c
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#include <esl_config.h>
#include "easel.h"
#include "esl_composition.h"
/* Function: esl_composition_BL62()
*
* Purpose: Sets <f> to the background frequencies used in
* \citep{Henikoff92} to calculate the BLOSUM62
* substitution matrix. Caller provides space in <f>
* allocated for at least 20 doubles. The entries are in
* alphabetic order A..Y, same as the standard Easel amino
* acid alphabet order.
*
* Returns: <eslOK> on success.
*/
int
esl_composition_BL62(double *f)
{
f[0] = 0.074;
f[1] = 0.025;
f[2] = 0.054;
f[3] = 0.054;
f[4] = 0.047;
f[5] = 0.074;
f[6] = 0.026;
f[7] = 0.068;
f[8] = 0.058;
f[9] = 0.099;
f[10] = 0.025;
f[11] = 0.045;
f[12] = 0.039;
f[13] = 0.034;
f[14] = 0.052;
f[15] = 0.057;
f[16] = 0.051;
f[17] = 0.073;
f[18] = 0.013;
f[19] = 0.032;
return eslOK;
}
/* Function: esl_composition_WAG()
*
* Purpose: Sets <f> to the background frequencies used in
* \citep{WhelanGoldman01} to calculate the WAG rate
* matrix. Caller provides space in <f> allocated for at
* least 20 doubles. The entries are in alphabetic order
* A..Y, same as the standard Easel amino acid alphabet
* order.
*
* Returns: <eslOK> on success.
*/
int
esl_composition_WAG(double *f)
{
f[0] = 0.086628; /* A */
f[1] = 0.019308; /* C */
f[2] = 0.057045; /* D */
f[3] = 0.058059; /* E */
f[4] = 0.038432; /* F */
f[5] = 0.083252; /* G */
f[6] = 0.024431; /* H */
f[7] = 0.048466; /* I */
f[8] = 0.062029; /* K */
f[9] = 0.086209; /* L */
f[10] = 0.019503; /* M */
f[11] = 0.039089; /* N */
f[12] = 0.045763; /* P */
f[13] = 0.036728; /* Q */
f[14] = 0.043972; /* R */
f[15] = 0.069518; /* S */
f[16] = 0.061013; /* T */
f[17] = 0.070896; /* V */
f[18] = 0.014386; /* W */
f[19] = 0.035274; /* Y */
return eslOK;
}
/* Function: esl_composition_SW34()
*
* Purpose: Sets <f> to the background frequencies observed in
* Swiss-Prot release 34 (21.2M residues). Caller provides
* space in <f> allocated for at least 20 doubles. The
* entries are in alphabetic order A..Y, same as the
* standard Easel amino acid alphabet order.
*
* Returns: <eslOK> on success.
*/
int
esl_composition_SW34(double *f)
{
f[0] = 0.075520; /* A */
f[1] = 0.016973; /* C */
f[2] = 0.053029; /* D */
f[3] = 0.063204; /* E */
f[4] = 0.040762; /* F */
f[5] = 0.068448; /* G */
f[6] = 0.022406; /* H */
f[7] = 0.057284; /* I */
f[8] = 0.059398; /* K */
f[9] = 0.093399; /* L */
f[10] = 0.023569; /* M */
f[11] = 0.045293; /* N */
f[12] = 0.049262; /* P */
f[13] = 0.040231; /* Q */
f[14] = 0.051573; /* R */
f[15] = 0.072214; /* S */
f[16] = 0.057454; /* T */
f[17] = 0.065252; /* V */
f[18] = 0.012513; /* W */
f[19] = 0.031985; /* Y */
return eslOK;
}
/* Function: esl_composition_SW50()
*
* Purpose: Sets <f> to the background frequencies observed in
* Swiss-Prot release 50.8 (86.0M residues; Oct 2006).
*
* Returns: <eslOK> on success.
*/
int
esl_composition_SW50(double *f)
{
f[0] = 0.0787945; /* A */
f[1] = 0.0151600; /* C */
f[2] = 0.0535222; /* D */
f[3] = 0.0668298; /* E */
f[4] = 0.0397062; /* F */
f[5] = 0.0695071; /* G */
f[6] = 0.0229198; /* H */
f[7] = 0.0590092; /* I */
f[8] = 0.0594422; /* K */
f[9] = 0.0963728; /* L */
f[10]= 0.0237718; /* M */
f[11]= 0.0414386; /* N */
f[12]= 0.0482904; /* P */
f[13]= 0.0395639; /* Q */
f[14]= 0.0540978; /* R */
f[15]= 0.0683364; /* S */
f[16]= 0.0540687; /* T */
f[17]= 0.0673417; /* V */
f[18]= 0.0114135; /* W */
f[19]= 0.0304133; /* Y */
return eslOK;
}