Search results for "Contig"
showing 8 items of 38 documents
High-Quality Whole-Genome Sequence of an Estradiol-Degrading Strain, Novosphingobium tardaugens NBRC 16725
2019
In this work we report the complete sequence and assembly of the estradiol-degrading bacterium Novosphingobium tardaugens NBRC 16725 genome into a single contig using the Pacific Biosciences RS II system.
MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study
2019
Abstract Motivation Metagenomes offer a glimpse into the total genomic diversity contained within a sample. Currently, however, there is no straightforward way to obtain a non-redundant list of all putative homologs of a set of reference sequences present in a metagenome. Results To address this problem, we developed a novel clustering approach called ‘metagenomic clustering by reference library’ (MCRL), where a reference library containing a set of reference genes is clustered with respect to an assembled metagenome. According to our proposed approach, reference genes homologous to similar sets of metagenomic sequences, termed ‘signatures’, are iteratively clustered in a greedy fashion, re…
SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files
2021
[Motivation]: Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user’s expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences’ analysis.
On rural development of NUTS 2 and 3: a non parametric approach of distribution dynamics analysis
2008
This work presents a study about dynamics of territorial gaps in agriculture between EU NUTS 2 and 3 from three perspectives: agricultural production model, rural development and productivity. Our choice of methodology is driven by two considerations. First of all, different performances in agriculture of EU areas may lead to multimodal distributions of indicators, and this implies that no significant average behaviour a parametric estimates refers to can be identified. Secondly, even if one wants to highlight multimodality within distributions, techniques like univariate density estimates can not catch intra-distribution dynamics which lead to the formation of "poles" of units showing a "s…
Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut
2013
Abstract Background The main limitations in the analysis of viral metagenomes are perhaps the high genetic variability and the lack of information in extant databases. To address these issues, several bioinformatic tools have been specifically designed or adapted for metagenomics by improving read assembly and creating more sensitive methods for homology detection. This study compares the performance of different available assemblers and taxonomic annotation software using simulated viral-metagenomic data. Results We simulated two 454 viral metagenomes using genomes from NCBI's RefSeq database based on the list of actual viruses found in previously published metagenomes. Three different ass…
Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations
2015
Metagenomic libraries consist of DNA fragments from diverse species, with varying genome size and abundance. High-throughput sequencing platforms produce large volumes of reads from these libraries, which may be assembled into contigs, ideally resembling the original larger genomic sequences. The uneven species distribution, along with the stochasticity in sample processing and sequencing bias, impacts the success of accurate sequence assembly. Several assemblers enable the processing of viral metagenomic data de novo, generally using overlap layout consensus or de Bruijn graph approaches for contig assembly. The success of viral genomic reconstruction in these datasets is limited by the de…
Sui modelli di incriminazione della contiguità alle organizzazioni criminali nel panorama europeo: appunti per un'auspicabile (ma improbabile?) rifor…
2010
Il saggio affronta la tormentata questione dei presuppostie e dei limiti del c.d. concorso esterno nel reato associativo, alla luce dei precedenti storici, di un'analisi comparativa in ambito europeo e dei più recenti approdi giurisprudenziali. Il lavoro si conclude con una proposta di riforma legislativa volta a tipizzare le condotte punibili nell'area della contiguità alle organizzazioni mafiose che tenga conto delle esigenze politico-criminali italiane e in sintonia con gli orientamenti dell'Unione europea.
An Examination of Tourist Arrivals Dynamics Using Short-Term Time Series Data: A Space—Time Cluster Approach
2013
The purpose of this study is to examine the development of Italian tourist areas ( circoscrizioni turistiche) through a cluster analysis of short time series. The technique is an adaptation of the functional data analysis approach developed by Abraham et al (2003), which combines spline interpolation with k-means clustering. The findings indicate the presence of two patterns (increasing and stable) averagely characterizing groups of territories. Moreover, tests of spatial contiguity suggest the presence of ‘space–time clusters’; that is, areas in the same ‘time cluster’ are also spatially contiguous. These findings appear to be more robust in particular for those series characterized by an…