Accuracy Assessment of Consensus Sequence from Shotgun Sequencing

Author(s):  
Lei M. Li
2020 ◽  
Vol 52 ◽  
pp. 55-61
Author(s):  
Ettore Potente ◽  
Cosimo Cagnazzo ◽  
Alessandro Deodati ◽  
Giuseppe Mastronuzzi

2019 ◽  
Vol 15 (01) ◽  
pp. 1-8
Author(s):  
Ashish C Patel ◽  
C G Joshi

Current data storage technologies cannot keep pace longer with exponentially growing amounts of data through the extensive use of social networking photos and media, etc. The "digital world” with 4.4 zettabytes in 2013 has predicted it to reach 44 zettabytes by 2020. From the past 30 years, scientists and researchers have been trying to develop a robust way of storing data on a medium which is dense and ever-lasting and found DNA as the most promising storage medium. Unlike existing storage devices, DNA requires no maintenance, except the need to store at a cool and dark place. DNA has a small size with high density; just 1 gram of dry DNA can store about 455 exabytes of data. DNA stores the informations using four bases, viz., A, T, G, and C, while CDs, hard disks and other devices stores the information using 0’s and 1’s on the spiral tracks. In the DNA based storage, after binarization of digital file into the binary codes, encoding and decoding are important steps in DNA based storage system. Once the digital file is encoded, the next step is to synthesize arbitrary single-strand DNA sequences and that can be stored in the deep freeze until use.When there is a need for information to be recovered, it can be done using DNA sequencing. New generation sequencing (NGS) capable of producing sequences with very high throughput at a much lower cost about less than 0.1 USD for one MB of data than the first sequencing technologies. Post-sequencing processing includes alignment of all reads using multiple sequence alignment (MSA) algorithms to obtain different consensus sequences. The consensus sequence is decoded as the reversal of the encoding process. Most prior DNA data storage efforts sequenced and decoded the entire amount of stored digital information with no random access, but nowadays it has become possible to extract selective files (e.g., retrieving only required image from a collection) from a DNA pool using PCR-based random access. Various scientists successfully stored up to 110 zettabytes data in one gram of DNA. In the future, with an efficient encoding, error corrections, cheaper DNA synthesis,and sequencing, DNA based storage will become a practical solution for storage of exponentially growing digital data.


Land ◽  
2019 ◽  
Vol 8 (12) ◽  
pp. 193
Author(s):  
Ali Alghamdi ◽  
Anthony R. Cummings

The implications of change on local processes have attracted significant research interest in recent times. In urban settings, green spaces and forests have attracted much attention. Here, we present an assessment of change within the predominantly desert Middle Eastern city of Riyadh, an understudied setting. We utilized high-resolution SPOT 5 data and two classification techniques—maximum likelihood classification and object-oriented classification—to study the changes in Riyadh between 2004 and 2014. Imagery classification was completed with training data obtained from the SPOT 5 dataset, and an accuracy assessment was completed through a combination of field surveys and an application developed in ESRI Survey 123 tool. The Survey 123 tool allowed residents of Riyadh to present their views on land cover for the 2004 and 2014 imagery. Our analysis showed that soil or ‘desert’ areas were converted to roads and buildings to accommodate for Riyadh’s rapidly growing population. The object-oriented classifier provided higher overall accuracy than the maximum likelihood classifier (74.71% and 73.79% vs. 92.36% and 90.77% for 2004 and 2014). Our work provides insights into the changes within a desert environment and establishes a foundation for understanding change in this understudied setting.


2015 ◽  
Vol 8 (3) ◽  
pp. 1593-1604 ◽  
Author(s):  
C. Bassani ◽  
C. Manzo ◽  
F. Braga ◽  
M. Bresciani ◽  
C. Giardino ◽  
...  

Abstract. Hyperspectral imaging provides quantitative remote sensing of ocean colour by the high spectral resolution of the water features. The HICO™ (Hyperspectral Imager for the Coastal Ocean) is suitable for coastal studies and monitoring. The accurate retrieval of hyperspectral water-leaving reflectance from HICO™ data is still a challenge. The aim of this work is to retrieve the water-leaving reflectance from HICO™ data with a physically based algorithm, using the local microphysical properties of the aerosol in order to overcome the limitations of the standard aerosol types commonly used in atmospheric correction processing. The water-leaving reflectance was obtained using the HICO@CRI (HICO ATmospherically Corrected Reflectance Imagery) atmospheric correction algorithm by adapting the vector version of the Second Simulation of a Satellite Signal in the Solar Spectrum (6SV) radiative transfer code. The HICO@CRI algorithm was applied on to six HICO™ images acquired in the northern Mediterranean basin, using the microphysical properties measured by the Acqua Alta Oceanographic Tower (AAOT) AERONET site. The HICO@CRI results obtained with AERONET products were validated with in situ measurements showing an accuracy expressed by r2 = 0.98. Additional runs of HICO@CRI on the six images were performed using maritime, continental and urban standard aerosol types to perform the accuracy assessment when standard aerosol types implemented in 6SV are used. The results highlight that the microphysical properties of the aerosol improve the accuracy of the atmospheric correction compared to standard aerosol types. The normalized root mean square (NRMSE) and the similar spectral value (SSV) of the water-leaving reflectance show reduced accuracy in atmospheric correction results when there is an increase in aerosol loading. This is mainly when the standard aerosol type used is characterized with different optical properties compared to the local aerosol. The results suggest that if a water quality analysis is needed the microphysical properties of the aerosol need to be taken into consideration in the atmospheric correction of hyperspectral data over coastal environments, because aerosols influence the accuracy of the retrieved water-leaving reflectance.


1993 ◽  
Vol 13 (9) ◽  
pp. 5805-5813 ◽  
Author(s):  
M M Wang ◽  
R Y Tsai ◽  
K A Schrader ◽  
R R Reed

Genes which mediate odorant signal transduction are expressed at high levels in neurons of the olfactory epithelium. The molecular mechanism governing the restricted expression of these genes likely involves tissue-specific DNA binding proteins which coordinately activate transcription through sequence-specific interactions with olfactory promoter regions. We have identified binding sites for the olfactory neuron-specific transcription factor, Olf-1, in the sequences surrounding the transcriptional initiation site of five olfactory neuron-specific genes. The Olf-1 binding sites described define the consensus sequence YTCCCYRGGGAR. In addition, we have identified a second binding site, the U site, in the olfactory cyclic nucleotide gated channel and type III cyclase promoters, which binds factors present in all tissue examined. These experiments support a model in which expression of Olf-1 in the sensory neurons coordinately activates a set of olfactory neuron-specific genes. Furthermore, expression of a subset of these genes may be modulated by additional binding factors.


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