With sharp increasing in biological sequences, the traditional sequence alignment methods become unsuitable and infeasible. It motivates a surge of fast alignment-free techniques for sequence analysis. Among these methods, many sorts of feature vector methods are established and applied to reconstruction of species phylogeny. The vectors basically consist of some typical numerical features for certain biological problems. The features may come from the primary sequences, secondary or three dimensional structures of macromolecules. In this study, we propose a novel numerical vector based on only primary sequences of organism to build their phylogeny. Three chemical and physical properties of primary sequences: purine, pyrimidine and keto are also incorporated to the vector. Using each property, we convert the nucleotide sequence into a new sequence consisting of only two kinds of letters. Therefore, three sequences are constructed according to the three properties. For each letter of each sequence we calculate the number of the letter, the average position of the letter and the variation of the position of the letter appearing in the sequence. Tested on several datasets related to mammals, viruses and bacteria, this new tool is fast in speed and accurate for inferring the phylogeny of organisms.

Classification of protein are crucial topics in biology. The number of protein sequences stored in databases increases sharply in the past decade. Traditionally, comparison of protein sequences is usually carried out through multiple sequence alignment methods. However, these methods may be unsuitable for clustering of protein sequences when gene rearrangements occur such as in viral genomes. The computation is also very time-consuming for large datasets with long genomes. In this paper, based on three important bio- chemical properties of amino acids: the hydropathy index, polar requirement and chemical composition of the side chain, we propose a 24 dimensional feature vector describing the composition of amino acids in protein sequences. Our method not only utilizes the chemical properties of amino acids but also counts on their numbers and positions. The results on beta-globin, mammals, and three virus datasets show that this new tool is fast and accurate for classifying proteins and inferring the phylogeny of organisms.

Let V be a hypersurface with an isolated singularity at the origin defined by the holomorphic function f : (Cn , 0) → (C, 0). The Yau algebra L(V ) is defined to be the Lie algebra of derivations of the moduli algebra A(V ) := On/(f, ∂f , · · · , ∂f ), ∂x1 ∂xn i.e., L(V ) = Der(A(V ), A(V )) and plays an important role in singularity theory. It is known that L(V ) is a finite dimensional Lie algebra and its dimension λ(V ) is called Yau number. In this article, we generalize the Yau algebra and introduce a new series of k-th Yau algebras Lk(V) which are defined to be the Lie algebras of derivations of the moduli algebras Ak(V) = On/(f,mkJ(f)),k ≥ 0, i.e., Lk(V) = Der(Ak(V),Ak(V)) and where m is the maximal ideal of On. In particular, it is Yau algebra when k = 0. The dimension of Lk(V ) is denoted by λk(V ). These numbers i.e., k-th Yau numbers λk(V ), are new numerical analytic invariants of an isolated singularity. In this paper we studied these new series of Lie algebras Lk(V ) and also compute the Lie algebras L1(V ) for fewnomial isolated singularities. We also formulate a sharp upper estimate conjecture for the λk(V ) of weighted homogeneous isolated hypersurface singularities and we prove this conjecture in case of k = 1 for large class of singularities.

Let V be a hypersurface with an isolated singularity at the origin de- fined by the holomorphic function f : (Cn, 0) → (C, 0). L(V ) is defined to be the Lie algebra of derivations of the moduli algebra A(V ) := On/(f, ∂f , · · · , ∂f ), i.e. ∂x1 ∂xn L(V ) = Der(A(V ), A(V )). The Lie algebra L(V ) is finite dimensional solvable alge- bra and plays an important role in singularity theory. L(V ) is called Yau algebra and λ(V ), the dimension of L(V ), is called Yau number. Fewnomial singularities are those which can be defined by n-nomial in n indeterminates. These singularities were inten- sively studied from a mirror symmetry point of view by many other mathematicians. Here we investigate these singularities from a Yau algebra point of view. In our previous work, we formulated a sharp upper estimate conjecture for the Yau numbers of weighted homogeneous isolated hypersurface singularities and proved that this conjecture holds for binomial isolated hypersurface singularities. In this paper we verify this conjecture for weighted homogeneous fewnomial surface singularities.

For every smooth complex projective variety W of dimension d and nonnegative Kodaira dimension, we show the existence of a universal constant m depending only on d and two natural invariants of the very general fibres of an Iitaka fibration of W such that the pluricanonical system |mK_W| defines an Iitaka fibration. This is a consequence of a more general result on polarized adjoint divisors. In order to prove these results we develop a generalized theory of pairs, singularities, log canonical thresholds, adjunction, etc.