Ricardo Alberich

An algebraic metric for phylogenetic trees

The definition of similarity measures for phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in databases, and the assessment of phylogenetic reconstruction methods. The transposition distance for fully resolved trees is a recent addition to the extensive collection of available metrics for comparing phylogenetic trees. In this work, we generalize the transposition metric from fully resolved to arbitrary phylogenetic trees, through a construction that involves an embedding of the set of phylogenetic trees (up to isomorphisms) with a fixed number of labeled leaves into a symmetric group. We also show that this transposition distance can be computed in linear time and we establish some of its basic properties.

MP-Align: alignment of metabolic pathways

BackgroundComparing the metabolic pathways of different species is useful for understanding metabolic functions and can help in studying diseases and engineering drugs. Several comparison techniques for metabolic pathways have been introduced in the literature as a first attempt in this direction. The approaches are based on some simplified representation of metabolic pathways and on a related definition of a similarity score (or distance measure) between two pathways. More recent comparative research focuses on alignment techniques that can identify similar parts between pathways.ResultsWe propose a methodology for the pairwise comparison and alignment of metabolic pathways that aims at providing the largest conserved substructure of the pathways under consideration. The proposed methodology has been implemented in a tool called MP-Align, which has been used to perform several validation tests. The results showed that our similarity score makes it possible to discriminate between different domains and to reconstruct a meaningful phylogeny from metabolic data. The results further demonstrate that our alignment algorithm correctly identifies subpathways sharing a common biological function.ConclusionThe results of the validation tests performed with MP-Align are encouraging. A comparison with another proposal in the literature showed that our alignment algorithm is particularly well-suited to finding the largest conserved subpathway of the pathways under examination.

Streamflow dynamics in a Mediterranean temporary river.

Abstract Mediterranean rivers are characterized by the irregularity of flow, harsh hydrological fluctuations and a profound transformation as the result of human activity. In this study, we investigate the streamflow response of a Mediterranean temporary river in which different groundwater, agriculture and urban contributions play an important role. Streamflow was measured at three nested gauging stations installed along Na Borges River, a lowland agricultural catchment (319 km2) on the island of Mallorca. Based on two hydrological years (2004/05 and 2005/06), potential evapotranspiration and surface water–groundwater interaction generated a succession of four different hydrological periods playing an important role in baseflow dynamics. The runoff coefficients were very low (<5%). At the event scale, groundwater also controlled runoff response, being very different according to hydrogeology, antecedent conditions and human impacts. During dry seasons, wastewater and karstic spring discharges maintain an influent regime into some streams. As a result, intense rainstorms in late summer generated water volumes over the impervious urban surfaces involved, with the result that quickflow was significant because the hydrological pathways were active. Citation Estrany, J., Garcia, C. & Alberich, R. (2010) Streamflow dynamics in a Mediterranean temporary river. Hydrol. Sci. J. 55(5), 717–736.

Metabolomics analysis: Finding out metabolic building blocks

In this paper we propose a new methodology for the analysis of metabolic networks. We use the notion of strongly connected components of a graph, called in this context metabolic building blocks. Every strongly connected component is contracted to a single node in such a way that the resulting graph is a directed acyclic graph, called a metabolic DAG, with a considerably reduced number of nodes. The property of being a directed acyclic graph brings out a background graph topology that reveals the connectivity of the metabolic network, as well as bridges, isolated nodes and cut nodes. Altogether, it becomes a key information for the discovery of functional metabolic relations. Our methodology has been applied to the glycolysis and the purine metabolic pathways for all organisms in the KEGG database, although it is general enough to work on any database. As expected, using the metabolic DAGs formalism, a considerable reduction on the size of the metabolic networks has been obtained, specially in the case of the purine pathway due to its relative larger size. As a proof of concept, from the information captured by a metabolic DAG and its corresponding metabolic building blocks, we obtain the core of the glycolysis pathway and the core of the purine metabolism pathway and detect some essential metabolic building blocks that reveal the key reactions in both pathways. Finally, the application of our methodology to the glycolysis pathway and the purine metabolism pathway reproduce the tree of life for the whole set of the organisms represented in the KEGG database which supports the utility of this research.

The Significance of the ProtDeform Score for Structure Prediction and Alignment

Background When a researcher uses a program to align two proteins and gets a score, one of her main concerns is how often the program gives a similar score to pairs that are or are not in the same fold. This issue was analysed in detail recently for the program TM-align with its associated TM-score. It was shown that because the TM-score is length independent, it allows a P-value and a hit probability to be defined depending only on the score. Also, it was found that the TM-scores of gapless alignments closely follow an Extreme Value Distribution (EVD). The program ProtDeform for structural protein alignment was developed recently and is characterised by the ability to propose different transformations of different protein regions. Our goal is to analyse its associated score to allow a researcher to have objective reasons to prefer one aligner over another, and carry out a better interpretation of the output. Results The study on the ProtDeform score reveals that it is length independent in a wider score range than TM-scores and that PD-scores of gapless (random) alignments also approximately follow an EVD. On the CASP8 predictions, PD-scores and TM-scores, with respect to native structures, are highly correlated (0.95), and show that around a fifth of the predictions have a quality as low as 99.5% of the random scores. Using the Gold Standard benchmark, ProtDeform has lower probabilities of error than TM-align both at a similar speed. The analysis is extended to homology discrimination showing that, again, ProtDeform offers higher hit probabilities than TM-align. Finally, we suggest using three different P-values according to the three different contexts: Gapless alignments, optimised alignments for fold discrimination and that for superfamily discrimination. In conclusion, PD-scores are at the very least as valuable for prediction scoring as TM-scores, and on the protein classification problem, even more reliable.

SINGLE-PUSHOUT TRANSFORMATION OF TOTAL ALGEBRAS

We characterize the pairs of partial homomorphisms of total Σ-algebras that have a pushout in the corresponding category, for an arbitrary signature Σ. This characterization provides the application condition for the single-pushout approach to the transformation of total algebras.

Correction: Metabolomics analysis: Finding out metabolic building blocks

[This corrects the article DOI: 10.1371/journal.pone.0177031.].