Automatic detection of anchor points for multiple sequence alignment

<p>Abstract</p> <p>Background</p> <p>Determining beforehand specific positions to align (<it>anchor points</it>) has proved valuable for the accuracy of automated multiple sequence alignment (MSA) software. This feature can be used manually to include biological expertise, or automatically, usually by pairwise similarity searches. <it>Multiple </it>local similarities are be expected to be more adequate, as more biologically relevant. However, even good multiple local similarities can prove incompatible with the ordering of an alignment.</p> <p>Results</p> <p>We use a recently developed algorithm to detect multiple local similarities, which returns subsets of positions in the sequences sharing similar contexts of appearence. In this paper, we describe first how to get, with the help of this method, subsets of positions that could form partial columns in an alignment. We introduce next a graph-theoretic algorithm to detect (and remove) positions in the partial columns that are inconsistent with a multiple alignment. Partial columns can be used, for the time being, as guide only by a few MSA programs: ClustalW 2.0, DIALIGN 2 and T-Coffee. We perform tests on the effect of introducing these columns on the popular benchmark BAliBASE 3.</p> <p>Conclusions</p> <p>We show that the inclusion of our partial alignment columns, as anchor points, improve on the whole the accuracy of the aligner ClustalW on the benchmark BAliBASE 3.</p

Stable Flags and the Riemann-Hilbert Problem

We tackle the Riemann-Hilbert problem on the Riemann sphere as stalk-wise logarithmic modifications of the classical R\"ohrl-Deligne vector bundle. We show that the solutions of the Riemann-Hilbert problem are in bijection with some families of local filtrations which are stable under the prescribed monodromy maps. We introduce the notion of Birkhoff-Grothendieck trivialisation, and show that its computation corresponds to geodesic paths in some local affine Bruhat-Tits building. We use this to compute how the type of a bundle changes under stalk modifications, and give several corresponding algorithmic procedures.Comment: 39 page

MS4 - Multi-Scale Selector of Sequence Signatures: An alignment-free method for classification of biological sequences

International audienc

Introducing Trait Networks to Elucidate the Fluidity of Organismal Evolution Using Palaeontological Data

International audienceExplaining the evolution of animals requires ecological, developmental, paleontological, and phylogenetic considerations because organismal traits are affected by complex evolutionary processes. Modeling a plurality of processes, operating at distinct timescales on potentially interdependent traits, can benefit from approaches that are complementary treatments to phylogenetics. Here, we developed an inclusive network approach, implemented in the command line software ComponentGrapher, and analyzed trait co-occurrence of rhinocerotoid mammals. We identified stable, unstable, and pivotal traits, as well as traits contributing to complexes, that may follow to a common developmental regulation, that point to an early implementation of the postcranial Bauplan among rhinocerotoids. Strikingly, most identified traits are highly dissociable, used repeatedly in distinct combinations and in different taxa, which usually do not form clades. Therefore, the genes encoding these traits are likely recruited into novel gene regulation networks during the course of evolution. Our evo-systemic framework, generalizable to other evolved organizations, supports a pluralistic modeling of organismal evolution, including trees and networks

EXPONENTS OF A MEROMORPHIC CONNECTION ON A COMPACT RIEMANN SURFACE

We give a general definition of the exponents of a meromorphic connection del on a holomorphic vector bundle E of rank n over a compact Riemann surface X. We prove that they can be computed as invariants of a vector bundle E(L) canonically attached to E, which we construct and call the Levelt bundle of E, and whose degree (equal to the sum of the exponents) we estimate by upper and lower bounds (Fuchs' relations). We use this definition to construct, for every linear differential equation on a compact Riemann surface (with regular or irregular singularities), the companion bundle of the equation, a vector bundle endowed with a meromorphic connection that is equivalent to the given equation and has precisely the same singularities and the same set of exponents.French CNR

For consideration as an Article in the Discoveries section of MBE Aging at evolutionary crossroads: longitudinal gene co-expression network analyses of proximal and ultimate causes of aging in bats

International audienceHow, when and why do organisms, their tissues and their cells age remain challenging issues, although researchers have identified multiple mechanistic causes of aging, and three major evolutionary theories have been developed to unravel the ultimate causes of organismal aging. A central hypothesis of these theories is that the strength of natural selection decreases with age. However, empirical evidence on when, why and how organisms age is phylogenetically limited, especially in natural populations. Here, we developed generic comparisons of gene co-expression networks that quantify and dissect the heterogeneity of gene co-expression in conspecific individuals from different age-classes to provide topological evidence about some mechanical and fundamental causes of organismal aging. We applied this approach to investigate the complexity of some proximal and ultimate causes of aging phenotypes in a natural population of the greater mouse-eared bat Myotis myotis, a remarkably long-lived species given its body size and metabolic rate, with available longitudinal blood transcriptomes. Myotis gene co-expression networks become increasingly fragmented with age, suggesting an erosion of the strength of natural selection and a general dysregulation of gene co-expression in aging bats. However, selective pressures remain sufficiently strong to allow successive emergence of homogeneous age-specific gene co-expression patterns, for at least seven years. Thus, older individuals from long-lived species appear to sit at an evolutionary crossroad: as they age, they experience both a decrease in the strength of natural selection and a targeted selection for very specific biological processes, further inviting to refine a central hypothesis in evolutionary aging theories