In the present work we perform a phenomenological analysis of the effective low energy models with Pati-Salam (PS) gauge symmetry derived in the context of D-branes. A main issue in these models arises from the fact that the right-handed fermions and the PS-symmetry breaking Higgs field transform identically under the PS symmetry, causing unnatural matter-Higgs mixing effects. We argue that this problem could be solved in particular D-brane setups where these fields arise in different intersections. We further observe that whenever a large Higgs mass term is generated in a particular class of mass spectra, a splitting mechanism -reminiscent of the doublet triplet splitting- may protect the neutral Higgs components from a heavy mass term. We analyze the implications of each individual representation which in principle is available in these models in order to specify the minimal spectrum required to build up a consistent PS model which reconciles the low energy data. A short discussion is devoted on the effects of stringy instanton corrections, particularly those generating missing Yukawa couplings and contributing to the fermion mass textures. We discuss the correlations of the intersecting D-brane spectra with those obtained from Gepner constructions and analyze the superpotential, the resulting mass textures and the low energy implications of some examples of the latter along the lines proposed above.
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