Current methods cannot tell us what the nature of the protein universe is concretely. They are based on different models of amino acid substitution and multiple sequence alignment which is an NP-hard problem and requires manual intervention. Protein structural analysis also gives a direction for mapping the protein universe. Unfortunately, now only a minuscule fraction of proteins' 3-dimensional structures are known. Furthermore, the phylogenetic tree representations are not unique for any existing tree construction methods. Here we develop a novel method to realize the nature of protein universe. We show the protein universe can be realized as a protein space in 60-dimensional Euclidean space using a distance based on a normalized distribution of amino acids. Every protein is in one-to-one correspondence with a point in protein space, where proteins with similar properties stay close together. Thus the distance between two points in protein space represents the biological distance of the corresponding two proteins. We also propose a natural graphical representation for inferring phylogenies. The representation is natural and unique based on the biological distances of proteins in protein space. This will solve the fundamental question of how proteins are distributed in the protein universe.

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In this paper, we introduce a motivic version of To¨en’s derived Hall algebra. Then we point out that the two kinds of Hall algebras in the sense of To¨en and Kontsevich–Soibelman, respectively, are Drinfeld dual pairs, not only in the classical case (by counting over finite fields) but also in the motivic version. Consequently they are canonically isomorphic. All proofs, including that for the most important associative property, are deduced in a self-contained way by analyzing the symmetry properties around the octahedral axiom, a method we used previously

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