194 research outputs found
Fast Spaced Seed Hashing
No full textHashing k-mers is a common function across many bioinformatics applications and it is widely used for indexing, querying and rapid similarity search. Recently, spaced seeds, a special type of pattern that accounts for errors or mutations, are routinely used instead of k-mers. Spaced seeds allow to improve the sensitivity, with respect to k-mers, in many applications, however the hashing of spaced seeds increases substantially the computational time. Hence, the ability to speed up hashing operations of spaced seeds would have a major impact in the field, making spaced seed applications not only accurate, but also faster and more efficient.
In this paper we address the problem of efficient spaced seed hashing. The proposed algorithm exploits the similarity of adjacent spaced seed hash values in an input sequence in order to efficiently compute the next hash. We report a series of experiments on NGS reads hashing using several spaced seeds. In the experiments, our algorithm can compute the hashing values of spaced seeds with a speedup, with respect to the traditional approach, between 1.6x to 5.3x, depending on the structure of the spaced seed
FSH: Fast spaced seed hashing exploiting adjacent hashes
No full textAbstract Background Patterns with wildcards in specified positions, namely spaced seeds, are increasingly used instead of k-mers in many bioinformatics applications that require indexing, querying and rapid similarity search, as they can provide better sensitivity. Many of these applications require to compute the hashing of each position in the input sequences with respect to the given spaced seed, or to multiple spaced seeds. While the hashing of k-mers can be rapidly computed by exploiting the large overlap between consecutive k-mers, spaced seeds hashing is usually computed from scratch for each position in the input sequence, thus resulting in slower processing. Results The method proposed in this paper, fast spaced-seed hashing (FSH), exploits the similarity of the hash values of spaced seeds computed at adjacent positions in the input sequence. In our experiments we compute the hash for each positions of metagenomics reads from several datasets, with respect to different spaced seeds. We also propose a generalized version of the algorithm for the simultaneous computation of multiple spaced seeds hashing. In the experiments, our algorithm can compute the hashing values of spaced seeds with a speedup, with respect to the traditional approach, between 1.6 × to 5.3 × , depending on the structure of the spaced seed. Conclusions Spaced seed hashing is a routine task for several bioinformatics application. FSH allows to perform this task efficiently and raise the question of whether other hashing can be exploited to further improve the speed up. This has the potential of major impact in the field, making spaced seed applications not only accurate, but also faster and more efficient. Availability The software FSH is freely available for academic use at: https://bitbucket.org/samu661/fsh/overview
Higher recall in metagenomic sequence classification exploiting Overlapping Reads
No full textAbstract Background In recent years several different fields, such as ecology, medicine and microbiology, have experienced an unprecedented development due to the possibility of direct sequencing of microbioimic samples. Among problems that researchers in the field have to deal with, taxonomic classification of metagenomic reads is one of the most challenging. State of the art methods classify single reads with almost 100% precision. However, very often, the performance in terms of recall falls at about 50%. As a consequence, state-of-the-art methods are indeed capable of correctly classify only half of the reads in the sample. How to achieve better performances in terms of overall quality of classification remains a largely unsolved problem. Results In this paper we propose a method for metagenomics CLassification Improvement with Overlapping Reads (CLIOR), that exploits the information carried by the overlapping reads graph of the input read dataset to improve recall, f-measure, and the estimated abundance of species. In this work, we applied CLIOR on top of the classification produced by the classifier Clark-l. Experiments on simulated and synthetic metagenomes show that CLIOR can lead to substantial improvement of the recall rate, sometimes doubling it. On average, on simulated datasets, the increase of recall is paired with an higher precision too, while on synthetic datasets it comes at expenses of a small loss of precision. On experiments on real metagenomes CLIOR is able to assign many more reads while keeping the abundance ratios in line with previous studies. Conclusions Our results showed that with CLIOR is possible to boost the recall of a state-of-the-art metagenomic classifier by inferring and/or correcting the assignment of reads with missing or erroneous labeling. CLIOR is not restricted to the reads classification algorithm used in our experiments, but it may be applied to other methods too. Finally, CLIOR does not need large computational resources, and it can be run on a laptop
N,N-dimethyl-4-amino-2,1,3-benzothiadiazole: synthesis and luminescent solvatochromism
No full text2,1,3-benzothiadiazole (BTD) derivatives were widely applied as herbicides, fungicides and antibacterial agents. The strong withdrawing ability of BTD and its fluorescent properties make it appealing also for the preparation of luminescent materials. Polymers containing the BTD fragment were successfully exploited for advances applications such as organic light-emitting diodes (OLEDs), dyes, solar and photovoltaic cells, as recently reported by B.A.D. Neto et al. [Eur. J. Org. Chem. (2013) 228].
To the best of our knowledge, a complete synthetic procedure for N,N-dimethyl-4-amino-2,1,3-benzothiadiazole (BTDNMe2) from the commercially available 2,1,3-benzothiadiazole was never reported. The only reference available dates back to 1976 and describes the thermal decomposition of the corresponding ammonium salt [N.M. Slavachevskaja et al., Pharm. Chem. J. 10 (1976) 327]. The synthetic route here proposed involves nitration of BTD in sulfonitric mixture, followed by reduction of the nitro-group and subsequent methylation with iodomethane. BTDNMe2 was isolated as dark red oil and it was fully characterized by means of nuclear magnetic resonance (NMR) and infrared spectroscopy. Solutions of BTDNMe2 in common organic solvents revealed to be appreciably luminescent in the visible range. The increase of dielectric constant caused a non-linear red shift of the absorption and emission maxima, an increase of the Stokes shift and a reduction of the photoluminescence quantum yield. The electronic transitions related to the absorption and emission properties were associated to the HOMO-LUMO energy gap by means of electrochemical measurements and DFT calculations. Finally, BTDNMe2 was successfully used for the preparation of luminescent doped polymethylmethacrylate samples with intense orange emission
Intense millisecond-long red luminescence from heteroleptic Cu(I) 2,1,3-benzothiadiazole complexes
No full textIntense red-emitting heteroleptic Cu(I) complexes were isolated using 2,1,3-benzothiadiazole (BTD) as N-donor ligand and triphenylphosphine, bis[(2-diphenylphosphino)phenyl] ether (DPEphos) or bis(diphenylphosphino)methane (dppm) as P-donors. The structures of two mononuclear and one dinuclear derivatives with one nitrogen and two phosphorus atoms in the Cu(I) coordination sphere were ascertained by means of X-ray diffraction, revealing an overall tetrahedral geometry at the solid state due to the direct interaction of the counterion with Cu(I). Upon excitation with UV and violet-blue light, the Cu(I) complexes exhibited emissions centred between 623 and 683 nm with photoluminescence quantum yields up to 46%. Lifetimes in the tens-thousands millisecond range were observed. The values resulted affected by the choice of the counterion, and an increase of up to 15% was observed passing from tetrafluoroborate to perchlorate in the mononuclear BTD complex with two PPh3 ligands. DFT calculations indicated that the lowest energy absorptions have charge transfer nature, from the {CuP2} fragments with the contributions of the P-bonded aryl substituents to an unoccupied π* orbital of BTD. The triplet→singlet emissions involve the metal centre, the phosphine ligands, and the occupied and empty orbitals of BTD
Luís Camargo, an author-illustrator and strategies of reading: in focus the training of reading children
No full textTrata-se de pesquisa de mestrado, cujo objetivo foi analisar as estratégias de leitura para a formação de crianças no Ensino Fundamental, a partir da análise de livros do autor-ilustrador Luís Camargo. O corpus foi constituído por cinco obras do autor, dentre elas: „Maneco Caneco Chapéu de Funil‟ (1980), „Panela de arroz‟ (1980) e „Bule de café‟ (1982), que formam a coleção „Maneco Caneco Chapéu de Funil‟, além de „Os pregadores do Rei João‟ (1985); „Ficar Junto‟ (1992) e um relato coletado informalmente que se constituiu como documento para a pesquisa. Algumas questões norteadoras da pesquisa foram: Como a concepção de criança e sua formação como leitor mirim influenciam no momento da criação das obras na visão de um escritor-ilustrador? Da mesma maneira como a visão de arte, literatura e leitura interferem nesse processo. Se trata de pesquisa bibliográfica e documental, com contribuições teóricas advindas dos estudos de alguns conceitos bakhtinianos e vigotskinianos. Autores como Bajard (2007); Hunt (2010); dentre outros, foram colaboradores na compreensão da leitura, literatura e suas representações em determinado tempo e espaço, assim como, Zilberman, Lajolo (2007), sobre o processo histórico da leitura e da literatura. Solé (1998); Girotto e Souza (2010), por sua vez foram essenciais acerca do Ensino das Estratégias de Leitura. Notamos como resultado que é as estratégias de leitura precisam estar presentes no trabalho do professor, para que as crianças vejam sentido em ler e sim, a formação e a concepção de leitor mirim influenciam a criação de livros literários pelos autores.It is a master's research, whose objective was to analyze reading strategies for the formation of children in elementary school, based on the analysis of books by author-illustrator Luís Camargo. The corpus consisted of five works by the author, among them: 'Maneco Caneco Chapéu de Funil' (1980), 'Panela de arroz' (1980) and 'Bule de café' (1982), which form the collection 'Maneco Caneco Chapéu de Funil', in addition to' Os Pregadores do Rei João'(1985); 'Ficar Junto' (1992) and an informally collected report that was constituted as a document for the research. Some guiding questions of the research were: How does the conception of a child and its formation as a young reader influence the creation of the works in the vision of a writer-illustrator? In the same way the vision of art, literature and reading interfere in this process. It is a bibliographical and documentary research, with theoretical contributions coming from the studies of some Bakhtinian and Vigotskinian concepts. Authors such as Bajard (2007); Hunt (2010); among others, were collaborators in the understanding of reading, literature and their representations in a certain time and space, as well as, Zilberman, Lajolo (2007), on the historical process of reading and literature. Solé (1998); Girotto and Souza (2010), in turn were essential about Teaching Strategies of Reading. We note as a result that reading strategies need to be present in the teacher's work, so that children see meaning in reading and yes, the formation and the conception of young reader influence the creation of literary books by authors.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq
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