Search results for "Biological classification"
showing 7 items of 7 documents
Chemodiversity of the Essential Oil from Leaves of Abies nebrodensis (Lojac.) Mattei
2016
Abies nebrodensis (Lojac.) Mattei (Pinaceae) is a species occurring in a very small population only in a restricted area of Sicily. Its taxonomic classification as different species has been object of discussion. In this work the chemical composition of the essential oil from the leaves is presented for the first time and compared to the essential oils from other euroasiatic species reported in literature. Peculiar characteristics of the essential oil of A. nebrodensis are highlighted.
Deep learning models for bacteria taxonomic classification of metagenomic data.
2018
Background An open challenge in translational bioinformatics is the analysis of sequenced metagenomes from various environmental samples. Of course, several studies demonstrated the 16S ribosomal RNA could be considered as a barcode for bacteria classification at the genus level, but till now it is hard to identify the correct composition of metagenomic data from RNA-seq short-read data. 16S short-read data are generated using two next generation sequencing technologies, i.e. whole genome shotgun (WGS) and amplicon (AMP); typically, the former is filtered to obtain short-reads belonging to a 16S shotgun (SG), whereas the latter take into account only some specific 16S hypervariable regions.…
Taxonomic Classification for Living Organisms Using Convolutional Neural Networks
2017
Taxonomic classification has a wide-range of applications such as finding out more about evolutionary history. Compared to the estimated number of organisms that nature harbors, humanity does not have a thorough comprehension of to which specific classes they belong. The classification of living organisms can be done in many machine learning techniques. However, in this study, this is performed using convolutional neural networks. Moreover, a DNA encoding technique is incorporated in the algorithm to increase performance and avoid misclassifications. The algorithm proposed outperformed the state of the art algorithms in terms of accuracy and sensitivity, which illustrates a high potential f…
The Subject Matter and Methods of Comparative Biochemistry
1994
The diversity of living organisms, the abundance of forms, colours and phenotypes, is one of the most impressive aspects of our world. Since ancient times, science has concerned itself with the ordering and classification of this diversity. At first, only those structures and processes which were recognizable without any special apparatus could be compared; the invention of the light microscope and the electron microscope introduced new dimensions and new opportunities for comparison. Finally, progress to the molecular level became possible with the development of methods of biochemical analysis. Different comparative biological disciplines arose, each with particular goals and methods. The…
Not just BLAST nt: WGS database joins the party
2019
AbstractSince its introduction in 1990 and with over 50k citations, the NCBI BLAST family has been an essential tool of in silico molecular biology. The BLAST nt database, based on the traditional divisions of GenBank, has been the default and most comprehensive database for nucleotide BLAST searches and for taxonomic classification software in metagenomics. Here we argue that this is no longer the case. Currently, the NCBI WGS database contains one billion reads (almost five times more than GenBank), and with 4.4 trillion nucleotides, WGS has about 14 times more nucleotides than GenBank. This ratio is growing with time. We advocate a change in the database paradigm in taxonomic classificat…
Towards a functional classification of the freshwater phytoplankton
2002
This paper considers the structure of freshwater phytoplankton assemblages and promotes a scheme of ‘vegetation recognition’, based upon the functional associations of species represented in the plankton. These groups are often polyphyletic, recognizing commonly shared adaptive features, rather than common phylogeny, to be the key ecological driver. Thirty-one such associations are outlined and the basic pattern of their distinctive ecologies is outlined. An invitation to other plankton scientists to assist in the development of this scheme is issued.
Goal Oriented Soil Mapping
2017
Abstract Soil mapping is very important for the correct implementation of sustainable land use management. In recent decades, soil mapping methods and data availability have increased exponentially, improving the quality of the maps produced. Despite these advances, local knowledge is a great source of information, refined for centuries and useful for soil mapping and the implementation of a sustainable land management. Local wisdom and experience should be an important aspect of soil mapping because farmers will be one of the major end-users of the maps produced and they should account for the farmers’ reality. However, several problems have been identified in the spatial correlation betwe…