- amino aid replaement models. - Amino aid replaement models (amino aid substitution models or ma-. - to build amino aid models in 1972. - and Eient Method for Estimating Amino Aid Substitution Models,". - 2 Amino aid substitution models 6. - 2.1 Amino aid sequenes and amino aid substitutions. - 2.3 Amino aid substitution models. - 2.4 Methods to estimate amino aid substitution models. - 2.4.2.2 Steps to build an amino aid substitution. - 3 Alignment splitting methods for estimating amino aid. - 3.2 Steps to build an amino aid substitution model by align- ment splitting method. - 2.1 An amino aid matrix. - 2.3 Time of estimating LG model from the 200 largest alignments 16 3.1 The owhart of the alignment splitting method. - 3.3 A ase of the tree-based splitting method. - 2.2 Example for amino aid substitutions. - splitting method. - based splitting method. - Aa Amino aid. - a partiular amino aid during protein synthesis. - oding region features also inlude amino aid translations.. - The amino aid model (the amino aid matrix) whih shows the. - amino aid subtitution rate is required to analyze the evolution of protein. - However, building an amino aid model is not an easy task.. - Many methods for estimating amino aid model, whih have been pro-. - ML methods are widely used to estimate amino aid substitution. - The time for onstruting the amino aid substitution by ML method is. - data set. - method when building amino aid substitution models. - ontain enough phylogeneti information to build up amino aid models.. - Figure 1.3: The distribution of the 200 largest alignments. - Chapter 2: An introdution to amino aid substitution models is presented.. - First, amino aid sequenes and amino aid substitutions are introdued.. - Next, amino aid substitution. - Final, we present methods to build amino aid. - Chapter 3: We propose methods for estimating amino aid substitution. - based splitting method based on BioNJ to estimate amino aid substitution. - In this hapter, we introdue amino aid substitution models. - Then, amino aid substi-. - to estimate amino aid substitution models.. - 2.1 Amino aid sequenes and amino aid substitu-. - An amino aid sequene, the primary struture of the protein, is strutured. - This dierene is alled the hange of amino aid sequenes or the evolution. - Eah odon speies a single amino aid in a protein. - in a gene an alter the amino aid sequene of the protein enoded by. - Table 2.1: The 20 most ommon amino aids in proteins are. - these hanges are alled amino aid substitutions on amino aid sequenes.. - There are dierent kinds of mutations when omparing two amino aid. - Substitutions: Replaing one amino aid by another in the sequene.. - T able 2.2: Example for amino aid substitutions. - T able 2.2 shows an example of amino aid mutations when omparing two. - The amino aid substitution proess an be desribed by Markov Mod-. - Let P ij (T ) is probability that amino aid i hanges amino aid j in the time T . - This ondition is that the rate matrix is independent for time, and amino aid replaements. - Seond, amino aid frequenies remain more or less the same during. - all i , j and T where π i is the frequeny of eah amino aid (or base).. - Amino aid substitution models are known as matries those 20 ∗ 20 matri-. - amino aid to another one. - of observing a hange from amino aid x to amino aid y ( x 6= y ) during a. - amino aid x is unhanged equals 1 + q xx dt = 1 − P. - Amino aid substitution matries are essential for inferring protein phy-. - Amino aid sub-. - 2.4 Methods to estimate amino aid substitution mod-. - step is that sequene is seleted, amino aid dierenes are deteted, and. - They built amino aid substitution mod-. - Figure 2.1 is an amino aid model used. - frequenies (alulated probabilities) of amino aid i mutation into one j. - Figure 2.1: An amino aid matrix - from the observation of. - In 1992, amino aid substitution model JTT was estimated by Jones et al. - Jones et al estimated a new amino aid substitution model for membrane. - Maximum likelihood methods are applied to estimate amino aid substi-. - aid substitution models. - 2.4.2.2 Steps to build an amino aid substitution model by maximum like-. - timate amino aid substitution models by ML method. - As usual, amino aid sites are assumed to evolve independently,. - rate 20 ∗ 20 matrix Q = q xy where q xy ( xy ) is the number of substitutions from amino aid x to amino aid y per time unit.. - Figure 2.2: The owhart of maximum likelihood methods. - the owhart to estimate amino aid substitution models using LG. - likelihood trees is the bottlenek in the estimating amino aid substitution. - timating amino aid models. - to estime an amino aid model are detailed. - Figure 3.1: The owhart of the alignment splitting method. - The owhart to estimate amino aid substitution models by using. - alignment splitting method. - time in building amino aid substitution model in ML methods. - 3.2 Steps to build an amino aid substitution model. - and onsequently resulting in wrong amino aid substitution models. - Figure 3.2: The distribution of alignments whih are reated. - Figure 3.4: The distribution of alignments whih are re-. - The qualities of amino aid models are presented with the maximum log. - ments with the tree-based splitting method. - between LG and LG_ 8 (using tree-based splitting method).The orre- lation between two matries is about 99%. - the tree-based splitting method with threshold K . - the random splitting method. - the tree-based splitting method. - between FLU and FLU_ 8 (using tree-based splitting method).The or- relation between two matries is about 99%. - Estimating amino aid substitution models is a ruial task in studying. - threshold K = 8 to estimate amino aid substitution models from large data sets.. - An Improved General Amino Aid Replaement. - Model of amino aid substitution in proteins enoded. - FLU, an amino aid sub-