Search results for " alignment"
showing 10 items of 587 documents
Evolutionary conserved mechanisms pervade structure and transcriptional modulation of allograft inflammatory factor-1 from sea anemone Anemonia virid…
2017
Gene family encoding allograft inflammatory factor-1 (AIF-1) is well conserved among organisms; however, there is limited knowledge in lower organisms. In this study, the first AIF-1 homologue from cnidarians was identified and characterised in the sea anemone Anemonia viridis. The full-length cDNA of AvAIF-1 was of 913 bp with a 5' -untranslated region (UTR) of 148 bp, a 3'-UTR of 315 and an open reading frame (ORF) of 450 bp encoding a polypeptide with149 amino acid residues and predicted molecular weight of about 17 kDa. The predicted protein possesses evolutionary conserved EF hand Ca2+ binding motifs, post-transcriptional modification sites and a 3D structure which can be superimposed …
Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters
2016
Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators. This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data par…
A giant type I polyketide synthase participates in zygospore maturation in Chlamydomonas reinhardtii
2017
Polyketide synthases (PKSs) occur in many bacteria, fungi and plants. They are highly versatile enzymes involved in the biosynthesis of a large variety of compounds including antimicrobial agents, polymers associated with bacterial cell walls and plant pigments. While harmful algae are known to produce polyketide toxins, sequences of the genomes of non-toxic algae, including those of many green algal species, have surprisingly revealed the presence of genes encoding type I PKSs. The genome of the model alga Chlamydomonas reinhardtii (Chlorophyta) contains a single type I PKS gene, designated PKS1 (Cre10.g449750), which encodes a giant PKS with a predicted mass of 2.3 MDa. Here, we show that…
Avoided motifs: short amino acid strings missing from protein datasets.
2020
Abstract According to the amino acid composition of natural proteins, it could be expected that all possible sequences of three or four amino acids will occur at least once in large protein datasets purely by chance. However, in some species or cellular context, specific short amino acid motifs are missing due to unknown reasons. We describe these as Avoided Motifs, short amino acid combinations missing from biological sequences. Here we identify 209 human and 154 bacterial Avoided Motifs of length four amino acids, and discuss their possible functionality according to their presence in other species. Furthermore, we determine two Avoided Motifs of length three amino acids in human proteins…
Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses
2017
The current literature reveals that the intrathalline coexistence of multiple microalgal taxa in lichens is more common than previously thought, and additional complexity is supported by the coexistence of bacteria and basidiomycete yeasts in lichen thalli. This replaces the old paradigm that lichen symbiosis occurs between a fungus and a single photobiont. The lichen Ramalina farinacea has proven to be a suitable model to study the multiplicity of microalgae in lichen thalli due to the constant coexistence of Trebouxia sp. TR9 and T. jamesii in long-distance populations. To date, studies involving phycobiont diversity within entire thalli are based on Sanger sequencing, but this method see…
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…