Search results for "alignment"
showing 10 items of 627 documents
MAGA: A Supervised Method to Detect Motifs From Annotated Groups in Alignments
2020
Multiple sequence alignments are usually phylogenetically driven. They are studied in the framework of evolution. But sometimes, it is interesting to study residue conservation at positions unconstrained by evolutionary rules. We present a supervised method to access a layer of information difficult to appreciate visually when many protein sequences are aligned. This new tool (MAGA; http://cbdm-01.zdv.uni-mainz.de/~munoz/maga/ ) locates positions in multiple sequence alignments differentially conserved in manually defined groups of sequences.
Using Genetic Algorithms for Optimizing the PPC in the Highway Horizontal Alignment Design.
2016
Various studies have emphasized the interesting advantages related to the use of new transition curves for improving the geometric design of highway horizontal alignments. In a previous paper, one of the writers proposed a polynomial curve, called a polynomial parametric curve (PPC), proving its efficiency in solving several design problems characterized by a very complex geometry (egg-shaped transition, transition between reversing circular curves, semidirect and inner-loop connections, and so on). The PPC also showed considerable advantages from a dynamic perspective, as evidenced by the analysis of the main dynamic variables related to motion (as well as rate of change of radial accelera…
Spatio-temporal deixis and cognitive models in early Indo-European
2018
AbstractThis paper is a comparative study based on the linguistic evidence in Vedic Sanskrit and Homeric Greek, aimed at reconstructing the space-time cognitive models used in the Proto-Indo-European language in a diachronic perspective. While it has been widely recognized that ancient Indo-European languages construed earlier (and past) events as in front of later ones, as predicted in the Time-Reference-Point mapping, it is less clear how in the same languages the passage took place from this ‘archaic’ Time-RP model or non-deictic sequence, in which future events are behind or follow the past ones in a temporal sequence, to the more recent ‘post-archaic’ Ego-RP model that is found only fr…
Genomic organization and promoter characterization of the gene encoding a putative endoplasmic reticulum chaperone, ERp29
2002
Abstract ERp29 is a soluble protein localized in the endoplasmic reticulum (ER) of eukaryotic cells, which is conserved in all mammalian species. The N-terminal domain of ERp29 displays sequence and structural similarity to the protein disulfide isomerase despite the lack of the characteristic double cysteine motif. Although the exact function of ERp29 is not yet known, it was hypothesized that it may facilitate folding and/or export of secretory proteins in/from the ER. ERp29 is induced by ER stress, i.e. accumulation of unfolded proteins in the ER. To gain an insight into the mechanisms regulating ERp29 expression we have cloned and characterized the rat ERp29 gene and studied in details …
A hybrid short read mapping accelerator
2013
Background The rapid growth of short read datasets poses a new challenge to the short read mapping problem in terms of sensitivity and execution speed. Existing methods often use a restrictive error model for computing the alignments to improve speed, whereas more flexible error models are generally too slow for large-scale applications. A number of short read mapping software tools have been proposed. However, designs based on hardware are relatively rare. Field programmable gate arrays (FPGAs) have been successfully used in a number of specific application areas, such as the DSP and communications domains due to their outstanding parallel data processing capabilities, making them a compet…
Calibration of the photon spectrometer PHOS of the ALICE experiment
2019
Journal of Instrumentation 14(05), P05025 - P05025 (2019). doi:10.1088/1748-0221/14/05/P05025
Measurement of spin-orbital angular momentum interactions in relativistic heavy-ion collisions
2020
The first evidence of spin alignment of vector mesons ($K^{*0}$ and $\phi$) in heavy-ion collisions at the Large Hadron Collider (LHC) is reported. The spin density matrix element $\rho_{00}$ is measured at midrapidity ($|y| <$ 0.5) in Pb-Pb collisions at a center-of-mass energy ($\sqrt{s_{\rm NN}}$) of 2.76 TeV with the ALICE detector. $\rho_{00}$ values are found to be less than 1/3 (1/3 implies no spin alignment) at low transverse momentum ($p_{\rm T} <$ 2 GeV/$c$) for $K^{*0}$ and $\phi$ at a level of 3$\sigma$ and 2$\sigma$, respectively. No significant spin alignment is observed for the $K^0_S$ meson (spin = 0) in Pb-Pb collisions and for the vector mesons in $pp$ collisions. The meas…
Genetic organization of the citCDEF locus and identification of mae and clyR genes from Leuconostoc mesenteroides.
1999
ABSTRACT In this paper, we describe two open reading frames coding for a NAD-dependent malic enzyme ( mae ) and a putative regulatory protein ( clyR ) found in the upstream region of citCDEFG of Leuconostoc mesenteroides subsp. cremoris 195. The transcriptional analysis of the citrate lyase locus revealed one polycistronic mRNA covering the mae and citCDEF genes. This transcript was detected only on RNA prepared from cells grown in the presence of citrate. Primer extension experiments suggest that clyR and the citrate lyase operon are expressed from a bidirectional A-T-rich promoter region located between mae and clyR.
Novel mutations of the MET proto-oncogene in papillary renal carcinomas.
1999
Hereditary papillary renal carcinoma (HPRC) is characterized by multiple, bilateral papillary renal carcinomas. Previously, we demonstrated missense mutations in the tyrosine kinase domain of the MET proto-oncogene in HPRC and a subset of sporadic papillary renal carcinomas. In this study, we screened a large panel of sporadic papillary renal carcinomas and various solid tumors for mutations in the MET proto-oncogene. Summarizing these and previous results, mutations of the MET proto-oncogene were detected in 17/129 sporadic papillary renal carcinomas but not in other solid tumors. We detected five novel missense mutations; three of five mutations were located in the ATP-binding region of t…
NOseq: amplicon sequencing evaluation method for RNA m6A sites after chemical deamination
2020
Abstract Methods for the detection of m6A by RNA-Seq technologies are increasingly sought after. We here present NOseq, a method to detect m6A residues in defined amplicons by virtue of their resistance to chemical deamination, effected by nitrous acid. Partial deamination in NOseq affects all exocyclic amino groups present in nucleobases and thus also changes sequence information. The method uses a mapping algorithm specifically adapted to the sequence degeneration caused by deamination events. Thus, m6A sites with partial modification levels of ∼50% were detected in defined amplicons, and this threshold can be lowered to ∼10% by combination with m6A immunoprecipitation. NOseq faithfully d…