BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

Jakó, Éena; Ari, Eszter; Ittzés, Péter; Horváth, Arnold; Podani, János

doi:10.1016/j.ympev.2009.04.019

Cited by 16 publications

(7 citation statements)

References 75 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For representation of biological macromolecules, generalized molecular codes and molecular descriptors were proposed and used for classification of functional and/or evolutionary relationships . In the applied method, the binary encoded sequence information is transformed into a compact analytical form, called the ICF of Boolean functions.…”

Section: Methodsmentioning

confidence: 99%

“…Otherwise, if there is a vector inside the generated sub‐cube with conflicting truth value, then the algorithm will go on with the minimal nodes of these conflicting vectors. The final result will be a graph, named as ICF‐graph .…”

Section: Methodsmentioning

confidence: 99%

“…From the distance matrix, the tree is inferred by neighbor‐joining method . The whole procedure that involves the ICF method to infer trees is called Boolean analysis abbreviated as BOOL‐AN (Figure ). Although, in principle, it is possible to apply a nucleotide or a protein substitution matrix when we calculate a distance matrix from the ICF molecular descriptors, here we did not distinguish any substitution types, so that all the nucleotide differences were considered without weighting.…”

Section: Methodsmentioning

confidence: 99%

“…The input sequence data (a); the sequence information is encoded to binary strings (b); the ICF graphs are calculated from each binary string representation of the sequences (c); distance calculation between ICF graphs (d); visualization: tree construction (UPGMA or NJ) (e); metric multidimensional scaling (PCoA) (f). This figure is a slightly modified version of a figure from a previous paper of the authors .…”

Section: Methodsmentioning

confidence: 99%

“…It means also that cluster analyses of tRNAs generally produced trees of lower quality . Here, we will use a discrete mathematical method, based on Boolean analysis (BOOL‐AN) of discrete objects and the Iterative Canonical Form (ICF) of Boolean functions , which is principally different from the known statistical or stochastic approaches in its basic assumptions. It takes advantage of the lattice structure of the n ‐dimensional Boolean space, as well as of the relations of partial order.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Classification of tRNA isoacceptor sequences by using graph‐based molecular descriptors

Ari

Jakó

2016

Journal of Chemometrics

Self Cite

View full text Add to dashboard Cite

A discrete mathematical method, Boolean analysis (or BOOL-AN), was used for evaluating of functional relationships within and between the families of transfer RNA sequences. The binary encoded sequence information of each transfer RNA was transformed into a compact analytical form, called the Iterative Canonical Form (ICF) of Boolean functions. This canonical form can also be represented as a non-complete bipartite graph and used then as a generalized molecular descriptor. What is important ICF graphs can be derived without restrictions concerning the number of nodes. Besides, the proposed molecular descriptors are unique, compact, and complete, allowing sequence reconstruction without loss of information. The method provides raw vector data for calculating distance matrices by using different metrics. In turn, the calculated distances can be analyzed by neighbor-joining or by unweighted pair group method to derive a tree, or by principal coordinates analysis to obtain a multidimensional scaling plot. The ability to arrange the functionally identical tRNA isoacceptors into exclusive groups, reflecting the relationships between 22 tRNA sets with different amino acid specificities, was tested on tRNA genes of Escherichia coli. Performance of the BOOL-AN was compared with other methods, including standard phylogenetic approaches and distance calculations, based on DNA sequences and chemical indices. The results of classification are represented by trees. We conclude that ICF-graph distance calculations and the BOOL-AN software were able to derive the most consistent tree for tRNA isoacceptors in comparison with other methods.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Classification of tRNA isoacceptor sequences by using graph‐based molecular descriptors

Ari

Jakó

2016

Journal of Chemometrics

Self Cite

View full text Add to dashboard Cite

show abstract

A Fish-specific Member of the TPPP Protein Family?

Orosz

2012

J Mol Evol

View full text Add to dashboard Cite

A eukaryotic protein family, the tubulin polymerization promoting proteins (TPPPs), has recently been identified. It has been termed after its first member, TPPP/p25 or TPPP1, which exhibits microtubule-stabilizing function and plays a role in neurodegenerative diseases. In mammalian genomes, two further paralogues, TPPP2 and TPPP3, can be found. In this article, I show that TPPP1 and TPPP3, but not TPPP2, are included in paralogons, on human chromosomes, Hsa5 and Hsa16, respectively. I suggest that the single non-vertebrate tppp gene was duplicated in the first round of whole-genome duplication in the vertebrate lineage giving rise to tppp1 and the precursor of tppp2/tppp3. The existence of a teleost fish-specific fourth paralogue, tppp4, has also been raised, but it is not supported by synteny analysis. Alternatively, the new group can be considered as the fish orthologue of TPPP2. The case that the new group is the consequence of the teleost fish-specific whole-genome duplication (3R) cannot be excluded.

show abstract

Novel algorithm for phylogenetic analysis of proteins: application to analysis of the evolution of H5N1 influenza viruses

Perovic

2013

J Math Chem

View full text Add to dashboard Cite

BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

Cited by 16 publications

References 75 publications

Classification of tRNA isoacceptor sequences by using graph‐based molecular descriptors

Classification of tRNA isoacceptor sequences by using graph‐based molecular descriptors

A Fish-specific Member of the TPPP Protein Family?

Novel algorithm for phylogenetic analysis of proteins: application to analysis of the evolution of H5N1 influenza viruses

Contact Info

Product

Resources

About