scholarly journals Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes

2019 ◽  
Author(s):  
Javier Tamames ◽  
Marta Cobo-Simón ◽  
Fernando Puente-Sánchez
Keyword(s):  
Functional Annotation ◽  
Direct Analysis ◽  
Sequencing Depth ◽  
Marker Genes ◽  
Functional Assignment ◽  
Functional Profiles ◽  
Taxonomic Annotation ◽  
Main Factor ◽  
The Way

AbstractMetagenomes can be analysed using different approaches and tools. One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the usage of assemblies or the direct analysis of raw sequence reads instead. Many instances of each approach can be found in the literature, but to the best of our knowledge no evaluation of their different performances has been carried on, and we question if their results are comparable. We have studied this point by analysing several real and mock metagenomes using different methodologies and tools, and comparing the resulting taxonomic and functional profiles. Our results show that database completeness is the main factor determining the performance of the methods relying on direct read assignment either by homology, k-mer composition or similarity to marker genes, while methods relying on assembly and assignment of predicted genes are most influenced by sequencing depth, that in turn determines the completeness of the assembly. Although differences exist, taxonomic profiles are rather similar between raw read assignment and assembly assignment methods, while they are more divergent for methods based on k-mers and marker genes. Regarding functional annotation, analysis of raw reads retrieves more functions, but it also makes a significant number of over-predictions. Assembly methods are more advantageous as the size of the metagenome grows bigger.

scholarly journals Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Javier Tamames ◽  
Marta Cobo-Simón ◽  
Fernando Puente-Sánchez
Keyword(s):  
Functional Annotation ◽  
Direct Analysis ◽  
Marker Genes ◽  
Functional Assignment ◽  
Homology Searching ◽  
Assembly Algorithms ◽  
Functional Profiles ◽  
Taxonomic Annotation ◽  
Main Factor ◽  
The Way

Abstract Background Metagenomes can be analysed using different approaches and tools. One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the use of assembly algorithms or the direct analysis of raw sequence reads instead by homology searching, k-mer analysys, or detection of marker genes. Many instances of each approach can be found in the literature, but to the best of our knowledge no evaluation of their different performances has been carried on, and we question if their results are comparable. Results We have analysed several real and mock metagenomes using different methodologies and tools, and compared the resulting taxonomic and functional profiles. Our results show that database completeness (the representation of diverse organisms and taxa in it) is the main factor determining the performance of the methods relying on direct read assignment either by homology, k-mer composition or similarity to marker genes, while methods relying on assembly and assignment of predicted genes are most influenced by metagenomic size, that in turn determines the completeness of the assembly (the percentage of read that were assembled). Conclusions Although differences exist, taxonomic profiles are rather similar between raw read assignment and assembly assignment methods, while they are more divergent for methods based on k-mers and marker genes. Regarding functional annotation, analysis of raw reads retrieves more functions, but it also makes a substantial number of over-predictions. Assembly methods are more advantageous as the size of the metagenome grows bigger.

scholarly journals Automatic Gene Function Prediction in the 2020’s

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1264
Author(s):  
Stavros Makrodimitris ◽  
Roeland C. H. J. van Ham ◽  
Marcel J. T. Reinders
Keyword(s):  
Functional Annotation ◽  
Protein Sequences ◽  
Research Area ◽  
Function Prediction ◽  
Research Field ◽  
Model Species ◽  
Large Step ◽  
Gene Functions ◽  
Performance Gains ◽  
The Way

The current rate at which new DNA and protein sequences are being generated is too fast to experimentally discover the functions of those sequences, emphasizing the need for accurate Automatic Function Prediction (AFP) methods. AFP has been an active and growing research field for decades and has made considerable progress in that time. However, it is certainly not solved. In this paper, we describe challenges that the AFP field still has to overcome in the future to increase its applicability. The challenges we consider are how to: (1) include condition-specific functional annotation, (2) predict functions for non-model species, (3) include new informative data sources, (4) deal with the biases of Gene Ontology (GO) annotations, and (5) maximally exploit the GO to obtain performance gains. We also provide recommendations for addressing those challenges, by adapting (1) the way we represent proteins and genes, (2) the way we represent gene functions, and (3) the algorithms that perform the prediction from gene to function. Together, we show that AFP is still a vibrant research area that can benefit from continuing advances in machine learning with which AFP in the 2020s can again take a large step forward reinforcing the power of computational biology.

scholarly journals MiCoP: Microbial Community Profiling method for detecting viral and fungal organisms in metagenomic samples

2018 ◽  
Author(s):  
Nathan LaPierre ◽  
Serghei Mangul ◽  
Mohammed Alser ◽  
Igor Mandric ◽  
Nicholas C. Wu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Human Microbiome ◽  
Real Data ◽  
Human Microbiome Project ◽  
Direct Analysis ◽  
Fungal Species ◽  
Reference Database ◽  
Marker Genes ◽  
Full Diversity ◽  
Community Profiling

AbstractBackgroundHigh throughput sequencing has spurred the development of metagenomics, which involves the direct analysis of microbial communities in various environments such as soil, ocean water, and the human body. Many existing methods based on marker genes or k-mers have limited sensitivity or are too computationally demanding for many users. Additionally, most work in metagenomics has focused on bacteria and archaea, neglecting to study other key microbes such as viruses and eukaryotes.ResultsHere we present a method, MiCoP (Microbiome Community Profiling), that uses fast-mapping of reads to build a comprehensive reference database of full genomes from viruses and eukaryotes to achieve maximum read usage and enable the analysis of the virome and eukaryome in each sample. We demonstrate that mapping of metagenomic reads is feasible for the smaller viral and eukaryotic reference databases. We show that our method is accurate on simulated and mock community data and identifies many more viral and fungal species than previously-reported results on real data from the Human Microbiome Project.ConclusionsMiCoP is a mapping-based method that proves more effective than existing methods at abundance profiling of viruses and eukaryotes in metagenomic samples. MiCoP can be used to detect the full diversity of these communities. The code, data, and documentation is publicly available on GitHub at: https://github.com/smangul1/MiCoP

scholarly journals COMBREX: COMputational BRidge to EXperiments

2011 ◽  
Vol 39 (2) ◽  
pp. 581-583 ◽  
Author(s):  
Richard J. Roberts
Keyword(s):  
Functional Annotation ◽  
Pilot Project ◽  
Bacterial Genomes ◽  
Functional Assignment ◽  
Biological Community

COMBREX (computational bridges to experimentation) is a project to engage the biological community in providing better functional annotation of genomes. In essence, the project involves the generation by computational biologists of a database of predicted functions for genes in bacterial genomes. Those genes for which no functional assignments have been proven experimentally are then open for bids by biochemists to test the predicted functions. High-priority genes are those for which no previous functional assignment has been made as well as those where uncharacterized examples are present in many genomes. A pilot project is running that focuses on bacterial and archaeal genomes.

scholarly journals MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Alexander Eng ◽  
Adrian J. Verster ◽  
Elhanan Borenstein
Keyword(s):  
Distributed Computing ◽  
Functional Annotation ◽  
Sequence Data ◽  
Metagenomic Data ◽  
Metagenomic Sequencing ◽  
Distributed Computing Systems ◽  
Annotation Pipeline ◽  
Shotgun Metagenomic Sequencing ◽  
End To End ◽  
Functional Profiles

Abstract Background Microbial communities have become an important subject of research across multiple disciplines in recent years. These communities are often examined via shotgun metagenomic sequencing, a technology which can offer unique insights into the genomic content of a microbial community. Functional annotation of shotgun metagenomic data has become an increasingly popular method for identifying the aggregate functional capacities encoded by the community’s constituent microbes. Currently available metagenomic functional annotation pipelines, however, suffer from several shortcomings, including limited pipeline customization options, lack of standard raw sequence data pre-processing, and insufficient capabilities for integration with distributed computing systems. Results Here we introduce MetaLAFFA, a functional annotation pipeline designed to take unfiltered shotgun metagenomic data as input and generate functional profiles. MetaLAFFA is implemented as a Snakemake pipeline, which enables convenient integration with distributed computing clusters, allowing users to take full advantage of available computing resources. Default pipeline settings allow new users to run MetaLAFFA according to common practices while a Python module-based configuration system provides advanced users with a flexible interface for pipeline customization. MetaLAFFA also generates summary statistics for each step in the pipeline so that users can better understand pre-processing and annotation quality. Conclusions MetaLAFFA is a new end-to-end metagenomic functional annotation pipeline with distributed computing compatibility and flexible customization options. MetaLAFFA source code is available at https://github.com/borenstein-lab/MetaLAFFA and can be installed via Conda as described in the accompanying documentation.

CITY COMMUNITY CENTRES AS CULTURAL INSTITUTIONS – THEIR PLACE IN CULTURE AND ECONOMY

2012 ◽  
Vol 166 (4) ◽  
pp. 186-192
Author(s):  
Agnieszka GIELATA
Keyword(s):  
Legal Regulations ◽  
Cultural Institutions ◽  
City Community ◽  
Main Culture ◽  
Transformation Processes ◽  
Community Centre ◽  
Main Factor ◽  
The Way

The object of this article is to define the position of community centres as cultural institutions functioning in boroughs. The author presents the differences in the way community centres are organised, which results from specific legal regulations, and also indicates some legislative deficiencies directly influencing their definition and scope of functions. Moreover, the author is of the opinion that the changes following the transformation processes which spread over our country significantly influenced the change in the perception of community centres as a kind of entertainment, to some extent making it necessary to tailor the offer addressed to the particular groups of culturally active recipients. According to Szlendak in the article, there are 29 main culture recipient groups distinguished in Poland. The acknowledgment of the groups’ needs as well as a proper and precise offer selected by community centre co-ordinators, in the author’s assumption, should be the main factor aiming at eliminating the lack of interest in the pro-gramme’s offer.

scholarly journals PENGARUH KECERDASAN INTELEKTUAL, KECERDASAN EMOSIONAL, DAN KECERDASAN SPIRITUAL TERHADAP KINERJA WIRAUSAHA MUSLIM DI KABUPATEN PURWAKARTA

2018 ◽  
Vol 5 (1) ◽  
pp. 8-18
Author(s):  
Ismail Ludin ◽  
H. Suherman Saleh ◽  
Dedeng Abdul Gani Amruloh
Keyword(s):  
Field Research ◽  
Islamic Perspective ◽  
Emotional Quotient ◽  
Analysis Instrument ◽  
The World ◽  
Main Factor ◽  
The Way

Islam is a comprehensive religion. Islam is not only discussing about the dimension of ukhrowi (hereafter) but also world. One of that dimension is practicing of entrepreneur. Practicing of entrepreneur is one of the way to get a performance’s successful. In Islamic perspective, the success of muslimpreneur performance is associated in word of Al falah. Al falah is a success concept for muslimpreneur in the world and hereafter. There are many factors that affect the success of muslimpreneur performance. Human intelligent as the main factor surrounding of that. According to the phenomenon, this research aims to examine the effect of intellectual, emotional, and spiritual quotient toward the muslimpreneur performance. This research used descriptive analityc method. The population of this research is the Islamic small entreprise in Purwakarta regent with 86 number of samples. Double-linier-regression is used as analysis instrument. Library and field research as the dimension of research through questionnaire. The result of this research indicates first, partially, the muslimpreneur performance is insignificantly affected by intellectual and emotional quotient variable. Only the spiritual quotient that significantly affects toward the muslimpreneur perfomance. Second, simultanously, the muslimpreneur performance is significantly affected by the variable of intellectual, emotional, and spiritual quotient. This research is limited in independend variable. Exploring the most essential independen variable should be done in order to get better result. Keywords : Intelellectul quotient, emotional quotient, spiritual quotient, muslimpreneur performance, and Al falah.

Self-sacrifice for in-group's history: A diachronic perspective

2018 ◽  
Vol 41 ◽  
Author(s):  
Maria Babińska ◽  
Michal Bilewicz
Keyword(s):  
Clinical Psychology ◽  
Historical Events ◽  
Emotional Events ◽  
Reciprocal Process ◽  
The Way

AbstractThe problem of extended fusion and identification can be approached from a diachronic perspective. Based on our own research, as well as findings from the fields of social, political, and clinical psychology, we argue that the way contemporary emotional events shape local fusion is similar to the way in which historical experiences shape extended fusion. We propose a reciprocal process in which historical events shape contemporary identities, whereas contemporary identities shape interpretations of past traumas.

What is the purpose of cognition?

2020 ◽  
Vol 43 ◽  
Author(s):  
Aba Szollosi ◽  
Ben R. Newell
Keyword(s):  
Infinite Number ◽  
Human Cognition ◽  
The Way

Abstract The purpose of human cognition depends on the problem people try to solve. Defining the purpose is difficult, because people seem capable of representing problems in an infinite number of ways. The way in which the function of cognition develops needs to be central to our theories.

Peculiarity Parameters

1976 ◽  
Vol 32 ◽  
pp. 233-254
Author(s):  
H. M. Maitzen
Keyword(s):  
Magnetic Field ◽  
Magnetic Fields ◽  
Theoretical Work ◽  
Observational Evidence ◽  
Rotator Model ◽  
Peculiar Behaviour ◽  
Field Spectrum ◽  
Oblique Rotator ◽  
Ap Stars ◽  
The Way

Ap stars are peculiar in many aspects. During this century astronomers have been trying to collect data about these and have found a confusing variety of peculiar behaviour even from star to star that Struve stated in 1942 that at least we know that these phenomena are not supernatural. A real push to start deeper theoretical work on Ap stars was given by an additional observational evidence, namely the discovery of magnetic fields on these stars by Babcock (1947). This originated the concept that magnetic fields are the cause for spectroscopic and photometric peculiarities. Great leaps for the astronomical mankind were the Oblique Rotator model by Stibbs (1950) and Deutsch (1954), which by the way provided mathematical tools for the later handling pulsar geometries, anti the discovery of phase coincidence of the extrema of magnetic field, spectrum and photometric variations (e.g. Jarzebowski, 1960).

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