Bacterial Protein Structures Reveal Phylum Dependent Divergence

Protein sequence space is vast compared to protein fold space. This raises important questions about how structures adapt to evolutionary changes in protein sequences. A growing trend is to regard protein fold space as a continuum rather than a series of discrete structures. From this perspective, homologous protein structures within the same functional classification should reveal a constant rate of structural drift relative to sequence changes. The clusters of orthologous groups (COG) classification system was used to annotate homologous bacterial protein structures in the Protein Data Bank (PDB). The structures and sequences of proteins within each COG were compared against each other to establish their relatedness. As expected, the analysis demonstrates a sharp structural divergence between the bacterial phyla Firmicutes and Proteobacteria. Additionally, each COG had a distinct sequence/structure relationship, indicating that different evolutionary pressures affect the degree of structural divergence. However, our analysis also shows the relative drift rate between sequence identity and structure divergence remains constant

Cubic Spline Interpolation Reveals Different Evolutionary Trends of Various Species

Instead of being uniform in each branch of the biological evolutionary tree, the speed of evolution, measured in the number of mutations over a fixed number of years, seems to be much faster or much slower than average in some branches of the evolutionary tree. This paper describes an evolutionary trend discovery algorithm that uses cubic spline interpolation for various branches of the evolutionary tree. As shown in an example, within the vertebrate evolutionary tree, human evolution seems to be currently speeding up while the evolution of chickens is slowing down. The new algorithm can automatically identify those branches and times when something unusual has taken place, aiding data analytics of evolutionary data

A Computational Study of the Evolution of Cretan and Related Scripts

Crete was the birthplace of several ancient writings, including the Cretan Hieroglyphs, the Linear A and the Linear B scripts. Out of these three only Linear B is deciphered. The sound values of the Cretan Hieroglyph and the Linear A symbols are unknown and attempts to reconstruct them based on Linear B have not been fruitful. In this paper, we compare the ancient Cretan scripts with four other Mediterranean and Black Sea scripts, namely Phoenician, South Arabic, Greek and Old Hungarian. We provide a computational study of the evolution of the three Cretan and four other scripts. This study encompasses a novel translation of the scripts to a DNA encoding, which enables the use of hypothetical evolutionary tree reconstruction algorithms from the area of bioinformatics

A Computational Study of the Evolution of Cretan and Related Scripts

Crete was the birthplace of several ancient writings, including the Cretan Hieroglyphs, the Linear A and the Linear B scripts. Out of these three only Linear B is deciphered. The sound values of the Cretan Hieroglyph and the Linear A symbols are unknown and attempts to reconstruct them based on Linear B have not been fruitful. In this paper, we compare the ancient Cretan scripts with four other Mediterranean and Black Sea scripts, namely Phoenician, South Arabic, Greek and Old Hungarian. We provide a computational study of the evolution of the three Cretan and four other scripts. This study encompasses a novel translation of the scripts to a DNA encoding, which enables the use of hypothetical evolutionary tree reconstruction algorithms from the area of bioinformatics

An Incremental Phylogenetic Tree Algorithm Based on Repeated Insertions of Species

In this paper, we introduce a new phylogenetic tree algorithm that generates phylogenetic trees by repeatedly inserting species one-by-one. The incremental phylogenetic tree algorithm can work on proteins or DNA sequences. Computer experiments show that the new algorithm is better than the commonly used UPGMA and Neighbor Joining algorithms

A Computational Model of the Spread of Ancient Human Populations Based on Mitochondrial DNA Samples

The extraction of mitochondrial DNA (mtDNA) from ancient human population samples provides important data for the reconstruction of population influences, spread and evolution from the Neolithic to the present. This paper presents a mtDNA-based similarity measure between pairs of human populations and a computational model for the evolution of human populations. In a computational experiment, the paper studies the mtDNA information from five Neolithic and Bronze Age populations, namely the Andronovo, the Bell Beaker, the Minoan, the Rössen and the Únětice populations. In the past these populations were identified as separate cultural groups based on geographic location, age and the use of, decoration or shape of cultural artifacts

Data Mining of Pancreatic Cancer Protein Databases

Data mining of protein databases poses special challenges because many protein databases are non- relational whereas most data mining and machine learning algorithms assume the input data to be a type of rela- tional database that is also representable as an ARFF file. We developed a method to restructure protein databases so that they become amenable for various data mining and machine learning tools. Our restructuring method en- abled us to apply both decision tree and support vector machine classifiers to a pancreatic protein database. The SVM classifier that used both GO term and PFAM families to characterize proteins gave us over 73% accuracy in predicting whether a protein is involved in pancreatic cancer

A Computational Translation of the Phaistos Disk

For over a century the text of the Phaistos Disk remained an enigma without a convincing translation. This paper presents a novel semi-automatic translation method that uses for the first time a recently discovered connection between the Phaistos Disk symbols and other ancient scripts, including the Old Hungarian alphabet. The connection between the Phaistos Disk script and the Old Hungarian alphabet suggested the possibility that the Phaistos Disk language may be related to Proto-Finno-Ugric, Proto-Ugric, or Proto-Hungarian. Using words and suffixes from those languages, it is possible to translate the Phaistos Disk text as an ancient sun hymn, possibly connected to a winter solstice ceremony

A mitochondrial DNA-based computational model of the spread of human populations

This paper presents a mitochondrial DNA-based computational model of the spread of human populations. The computation model is based on a new measure of the relatedness of two populations that may be both heterogeneous in terms of their set of mtDNA haplogroups. The measure gives an exponentially increasing weight for the similarity of two haplogroups with the number of levels shared in the mtDNA classification tree. In an experiment, the computational model is applied to the study of the relatedness of seven human populations ranging from the Neolithic through the Bronze Age to the present. The human populations included in the computational study are the Andronovo, the Bell Beaker, the medieval Hungarian, the Khanty, the Minoan, the Rössen and the Únětice populations

A mitochondrial DNA-based computational model of the spread of human populations

This paper presents a mitochondrial DNA-based computational model of the spread of human populations. The computation model is based on a new measure of the relatedness of two populations that may be both heterogeneous in terms of their set of mtDNA haplogroups. The measure gives an exponentially increasing weight for the similarity of two haplogroups with the number of levels shared in the mtDNA classification tree. In an experiment, the computational model is applied to the study of the relatedness of seven human populations ranging from the Neolithic through the Bronze Age to the present. The human populations included in the computational study are the Andronovo, the Bell Beaker, the medieval Hungarian, the Khanty, the Minoan, the Rössen and the Únětice populations