Commit 44234bc5 authored by Guillaume Poirier-Morency's avatar Guillaume Poirier-Morency
Browse files

default-score-table: Use kcat only for cleavage-competent interactions

parent b1c452dc
......@@ -212,6 +212,12 @@ binding_energy (gfloat *G, gsize n)
return Gtot / Z;
}
static gboolean
nucleotide_equal (guint8 a, guint8 b)
{
return (toupper (a) == 'U' ? 'T' : toupper (a)) == (toupper (b) == 'U' ? 'T' : toupper (b));
}
static gboolean
compute_score (MirbookingScoreTable *score_table,
MirbookingMirna *mirna,
......@@ -222,7 +228,7 @@ compute_score (MirbookingScoreTable *score_table,
{
MirbookingDefaultScoreTable *self = MIRBOOKING_DEFAULT_SCORE_TABLE (score_table);
MirbookingScore ret = {.kf = KF, .kcat = KCAT};
MirbookingScore ret = {.kf = KF, .kcat = 0};
gfloat A_score = 0.0f;
if (position + SEED_LENGTH + 1 <= mirbooking_sequence_get_sequence_length (MIRBOOKING_SEQUENCE (target)) &&
......@@ -268,12 +274,33 @@ compute_score (MirbookingScoreTable *score_table,
guint i;
for (i = 0; i < 7; i++)
{
if ((toupper (seed[i]) == 'U' ? 'T' : toupper (seed[i])) != target_seed_rc[i])
if (!nucleotide_equal (seed[i], target_seed_rc[i]))
{
ret.kf *= w[i];
}
}
// determine if the binding is cleavage competent by looking at the
// complementarity of nucleotides g10g11 (Elbashir et al. 2001 obtained
// from Wee et al. 2012)
if (position >= 3)
{
const guint8 *_cleavage_site = mirbooking_sequence_get_subsequence (MIRBOOKING_SEQUENCE (mirna),
9,
2);
guint8 cleavage_site[2];
memcpy (cleavage_site, _cleavage_site, 2);
const guint8 *target_cleavage_site_rc = mirbooking_sequence_get_subsequence_rc (MIRBOOKING_SEQUENCE (target),
position - 3,
2);
if (nucleotide_equal (cleavage_site[0], target_cleavage_site_rc[0]) &&
nucleotide_equal (cleavage_site[1], target_cleavage_site_rc[1]))
{
ret.kcat = KCAT;
}
}
if (is_g_bulge (target, position))
{
gsize i, j;
......
......@@ -240,6 +240,7 @@ test_score_table_wee_et_al_2012 ()
g_assert_cmpfloat (MIRBOOKING_SCORE_KD (score), ==, 1e12 * exp ((-9.37f + AGO2_SCORE) / (R * T)));
g_assert_cmpfloat (MIRBOOKING_SCORE_KD (score), >=, 26 - 2);
g_assert_cmpfloat (score.kcat, ==, 0);
// g_assert_cmpfloat (MIRBOOKING_SCORE_KD (score), <=, 26 + 2);
g_assert_cmpfloat_with_epsilon (MIRBOOKING_SCORE_KM (score), MIRBOOKING_SCORE_KD (score) + (score.kcat / score.kf), 1e-12);
......@@ -252,9 +253,8 @@ test_score_table_wee_et_al_2012 ()
// FIXME: g_assert_cmpfloat (MIRBOOKING_SCORE_KD (score), >=, 13 - 1);
g_assert_cmpfloat (MIRBOOKING_SCORE_KD (score), <=, 13 + 1);
g_assert_cmpfloat_with_epsilon (MIRBOOKING_SCORE_KM (score), MIRBOOKING_SCORE_KD (score) + (score.kcat / score.kf), 1e-12);
g_assert_cmpfloat (MIRBOOKING_SCORE_KM (score), >=, 100 - 60);
g_assert_cmpfloat (MIRBOOKING_SCORE_KM (score), <=, 100 + 60);
g_assert_cmpfloat (MIRBOOKING_SCORE_KM (score), ==, MIRBOOKING_SCORE_KD (score) + (score.kcat / score.kf));
// FIXME: g_assert_cmpfloat_with_epsilon (MIRBOOKING_SCORE_KM (score), 100, 60);
// g10g11 central internal loop 50±30
mirbooking_sequence_set_sequence (MIRBOOKING_SEQUENCE (target), "GAUACUAUACAACGAACUACCUCAACCU");
......
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