Search results for " sequence"
showing 10 items of 3643 documents
Balanced Words Having Simple Burrows-Wheeler Transform
2009
The investigation of the "clustering effect" of the Burrows-Wheeler transform (BWT) leads to study the words having simple BWT , i.e. words w over an ordered alphabet $A=\{a_1,a_2,\ldots,a_k\}$, with $a_1 < a_2 < \ldots <a_k$, such that $bwt(w)$ is of the form $a_k^{n_k} a_{k-1}^{n_{k-1}} \cdots a_1^{n_1}$, for some non-negative integers $n_1, n_2, \ldots, n_k$. We remark that, in the case of binary alphabets, there is an equivalence between words having simple BWT, the family of (circular) balanced words and the conjugates of standard words. In the case of alphabets of size greater than two, there is no more equivalence between these notions. As a main result of this paper we prove that, u…
Variations on a Theorem of Fine & Wilf
2001
In 1965, Fine & Wilf proved the following theorem: if (fn)n≥0 and (gn)n≥0 are periodic sequences of real numbers, of periods h and k respectively, and fn = gn for 0 ≤ n ≤ h+k-gcd(h, k), then fn = gn for all n ≥ 0. Furthermore, the constant h + k - gcd(h, k) is best possible. In this paper we consider some variations on this theorem. In particular, we study the case where fn ≤ gn instead of fn = gn. We also obtain a generalization to more than two periods.
Type and Cotype in Vector-Valued Nakano Sequence Spaces
2001
AbstractGiven a sequence of Banach spaces {Xn}n and a sequence of real numbers {pn}n in [1,∞), the vector-valued Nakano sequence spaces ℓ({pn},{Xn}) consist of elements {xn}n in ∏nXn for which there is a constant λ>0 such that ∑n(‖xn‖/λ)pn<∞. In this paper we find the conditions on the Banach spaces Xn and on the sequence {pn}n for the spaces ℓ({pn},{Xn}) to have cotype q or type p.
Copy number variation and missense mutations of the agouti signaling protein (ASIP) gene in goat breeds with different coat colors.
2009
In goats, classical genetic studies reported a large number of alleles at the Agouti locus with effects on coat color and pattern distribution. From these early studies, the dominant A(Wt) (white/tan) allele was suggested to cause the white color of the Saanen breed. Here, we sequenced the coding region of the goat ASIP gene in 6 goat breeds (Girgentana, Maltese, Derivata di Siria, Murciano-Granadina, Camosciata delle Alpi, and Saanen), with different coat colors and patterns. Five single nucleotide polymorphisms (SNPs) were identified, 3 of which caused missense mutations in conserved positions of the cysteine-rich carboxy-terminal domain of the protein (p.Ala96Gly, p.Cys126Gly, and p.Val1…
Comparative genomics and protein domain graph analyses link ubiquitination and RNA metabolism.
2006
The human gene parkin, known to cause familial Parkinson disease, as well as several other genes, likely involved in other neurodegenerative diseases or in cancer, encode proteins of the RBR family of ubiquitin ligases. Here, we describe the structural diversity of the RBR family in order to infer their functional roles. Of particular interest is a relationship detected between RBR-mediated ubiquitination and RNA metabolism: a few RBR proteins contain RNA binding domains and DEAH-box RNA helicase domains. Global protein domain graph analyses demonstrate that this connection is not RBR-specific, but instead many other proteins contain both ubiquitination and RNA-related domains. These protei…
Factors Behind Junk DNA in Bacteria
2012
Although bacterial genomes have been traditionally viewed as being very compact, with relatively low amounts of repetitive and non-coding DNA, this view has dramatically changed in recent years. The increase of available complete bacterial genomes has revealed that many species present abundant repetitive DNA (i.e., insertion sequences, prophages or paralogous genes) and that many of these sequences are not functional but can have evolutionary consequences as concerns the adaptation to specialized host-related ecological niches. Comparative genomics analyses with close relatives that live in non-specialized environments reveal the nature and fate of this bacterial junk DNA. In addition, the…
Perdió el libro que se compró / había comprado pocos días antes: Reflexiones iniciales en torno al saber gramatical sobre los tiempos verbales del pa…
2007
Carmen.Rdez-Gonzalo@uv.es La alternancia entre los tiempos verbales del pasado en textos escritos exige tener en cuenta diferencias aspectuales poco presentes en el español hablado. Según López García (2005: 162), el sistema de cinco tiempos simples (vengo, venía, vine, vendría, vendré) cubre las necesidades expresivas de los hispanohablantes, aunque los niños emplean menos y muchos hablantes adultos raramente usan otras formas. Los problemas se plantean cuando en lugar de hablar español necesitamos escribirlo y leerlo. Esta necesidad cambia por completo el inventario de tiempos ya que, para articular un texto es preciso dejar muy claro que unos acontecimientos ocurren antes o después de ot…
Third-order iterative methods without using any Fréchet derivative
2003
AbstractA modification of classical third-order methods is proposed. The main advantage of these methods is they do not need to evaluate any Fréchet derivative. A convergence theorem in Banach spaces, just assuming the second divided difference is bounded and a punctual condition, is analyzed. Finally, some numerical results are presented.
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes
2009
Abstract Background ESTs or variable sequence reads can be available in prokaryotic studies well before a complete genome is known. Use cases include (i) transcriptome studies or (ii) single cell sequencing of bacteria. Without suitable software their further analysis and mapping would have to await finalization of the corresponding genome. Results The tool JANE rapidly maps ESTs or variable sequence reads in prokaryotic sequencing and transcriptome efforts to related template genomes. It provides an easy-to-use graphics interface for information retrieval and a toolkit for EST or nucleotide sequence function prediction. Furthermore, we developed for rapid mapping an enhanced sequence align…
Homology of pseudodifferential operators on manifolds with fibered cusps
2003
The Hochschild homology of the algebra of pseudodifferential operators on a manifold with fibered cusps, introduced by Mazzeo and Melrose, is studied and computed using the approach of Brylinski and Getzler. One of the main technical tools is a new convergence criterion for tri-filtered half-plane spectral sequences. Using trace-like functionals that generate the 0 0 -dimensional Hochschild cohomology groups, the index of a fully elliptic fibered cusp operator is expressed as the sum of a local contribution of Atiyah-Singer type and a global term on the boundary. We announce a result relating this boundary term to the adiabatic limit of the eta invariant in a particular case.