109 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
Samuele R. Bacchiocchi and Family
No full textSeventh-day Adventist author and theologian, Samuele R. Bacchiocchi and his wife and their children at a graduation ceremony at Pontifical University
sd920/FIJI-macros-for-IHC-and-SHG-analysis: Batch Split Channels (3 channels)
No full textThis macro allows to split channels for Z-stack .tiff files and save them in a new folder in batch mode.
Author: Samuele Di Carmine, [email protected]
Version 1.0
July 13, 2021
//License: BSD3
Copyright 2021 Samuele Di Carmine, Imperial College Londo
Samuele R. Bacchiocchi
No full textSamuele R. Bacchiocchi was a Seventh-day Adventist author and theologian best known for his work on the Sabbath in Christianity, particularly in the historical work "From Sabbath to Sunday," based on his doctoral thesis from the Pontifical Gregorian University. Bacchiocchi defended the validity of the Feasts of the Lord, situated in Leviticus 23. He wrote two books on the subject. He was also known within the Seventh-day Adventist church for his opposition to rock and contemporary Christian music, jewelry, the celebration of Christmas and Easter, certain dress standards, and alcohol. This photograph was taken during a graduation ceremony from Pontifical University
The Impact of the COVID-19 Emergency on Local Vehicular Traffic and Its Consequences for the Environment: The Case of the City of Reggio Emilia (Italy)
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Open AccessArticle
The Impact of the COVID-19 Emergency on Local Vehicular Traffic and Its Consequences for the Environment: The Case of the City of Reggio Emilia (Italy)
by Samuele Marinello 1,*OrcID,Francesco Lolli 1,2 andRita Gamberini 1,2OrcID
1
En&Tech Interdepartmental Center, University of Modena and Reggio Emilia, 42124 Reggio Emilia, Italy
2
Department of Sciences and Methods for Engineering, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy
*
Author to whom correspondence should be addressed.
Sustainability 2021, 13(1), 118; https://doi.org/10.3390/su13010118
Received: 3 December 2020 / Revised: 21 December 2020 / Accepted: 22 December 2020 / Published: 24 December 2020
(This article belongs to the Special Issue 8th World Sustainability Forum—Selected Papers)
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Abstract
The COVID-19 health emergency has imposed the need to limit and/or stop non-essential economic and commercial activities and movement of people. The objective of this work is to report an assessment of the change in vehicle flows and in air quality of a specific study area in the north of Italy, comparing the periods February–May 2020 and February–May 2019. Circulating vehicles have been measured at nine characteristic points of the local road network of the city of Reggio Emilia (Italy), while atmospheric pollutant concentrations have been analysed using data extracted from the regional air quality monitoring network. The results highlight a rapid decline in the number of vehicles circulating in 2020 (with values of up to −82%). This has contributed to a reduction in air concentrations of pollutants, in particular for NO2 and CO (over 30% and over 22%, respectively). On the other hand, O3 has increased (by about +13%), but this is expected. Finally, the particulate matter grew (about 30%), with a behaviour similar to the whole regional territory. The empirical findings of this study provide some indications and useful information to assist in understanding the effects of traffic blocking in urban areas on air quality
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