Search results for "Annotation"
showing 10 items of 161 documents
NeoFox: annotating neoantigen candidates with neoantigen features
2020
Abstract Summary The detection and prediction of true neoantigens is of great importance for the field of cancer immunotherapy. Wesearched the literature for proposed neoantigen features and integrated them into a toolbox called NEOantigen Feature toolbOX (NeoFox). NeoFox is an easy-to-use Python package that enables the annotation of neoantigen candidates with 16 neoantigen features. Availability and implementation NeoFox is freely available as an open source Python package released under the GNU General Public License (GPL) v3 license at https://github.com/TRON-Bioinformatics/neofox. Supplementary information Supplementary data are available at Bioinformatics online.
Discourse Markers in Speech: Distinctive Features and Corpus Annotation
2017
It is generally acknowledged that discourse markers are used differently in speech and writing, yet many general descriptions and most annotation frameworks are written-based, thus partially unfit to be applied in spoken corpora. This paper identifies the major distinctive features of discourse markers in spoken language, which can be associated with problems related to their scope and structure, their meaning and their tendency to co-occur. The description is based on authentic examples and is followed by methodological recommendations on how to deal with these phenomena in more exhaustive, speech-friendly annotation models.
Domain Expert Platform for Goal-Oriented Dialog Collection
2021
Today, most dialogue systems are fully or partly built using neural network architectures. A crucial prerequisite for the creation of a goal-oriented neural network dialogue system is a dataset that represents typical dialogue scenarios and includes various semantic annotations, e.g. intents, slots and dialogue actions, that are necessary for training a particular neural network architecture. In this demonstration paper, we present an easy to use interface and its back-end which is oriented to domain experts for the collection of goal-oriented dialogue samples. The platform not only allows to collect or write sample dialogues in a structured way, but also provides a means for simple annotat…
Biotechnological potential of respiring Zymomonas mobilis: a stoichiometric analysis of its central metabolism.
2013
The active, yet energetically inefficient electron transport chain of the ethanologenic bacterium Zymomonas mobilis could be used in metabolic engineering for redox-balancing purposes during synthesis of certain products. Although several reconstructions of Z. mobilis metabolism have been published, important aspects of redox balance and aerobic catabolism have not previously been considered. Here, annotated genome sequences and metabolic reconstructions have been combined with existing biochemical evidence to yield a medium-scale model of Z. mobilis central metabolism in the form of COBRA Toolbox model files for flux balance analysis (FBA). The stoichiometric analysis presented here sugges…
Symbolic Reductionist Model for Program Comprehension
2007
This article presents the main features of a novel construction, symbolic analysis, for automatic source code processing. The method is superior to the known methods, because it uses a semiotic, interpretative approach. Its most important processes and characteristics are considered here. We describe symbolic information retrieval and the process of analysis in which it can be used in order to obtain pragmatic information. This, in turn, is useful in understanding a current Java program version when developing a new version.
Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut
2013
Abstract Background The main limitations in the analysis of viral metagenomes are perhaps the high genetic variability and the lack of information in extant databases. To address these issues, several bioinformatic tools have been specifically designed or adapted for metagenomics by improving read assembly and creating more sensitive methods for homology detection. This study compares the performance of different available assemblers and taxonomic annotation software using simulated viral-metagenomic data. Results We simulated two 454 viral metagenomes using genomes from NCBI's RefSeq database based on the list of actual viruses found in previously published metagenomes. Three different ass…
Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution
2014
Background The different regions of a genome do not evolve at the same rate. For example, comparative genomic studies have suggested that the sex chromosomes and the regions harbouring the immune defence genes in the Major Histocompatability Complex (MHC) may evolve faster than other genomic regions. The advent of the next generation sequencing technologies has made it possible to study which genomic regions are evolutionary liable to change and which are static, as well as enabling an increasing number of genome studies of non-model species. However, de novo sequencing of the whole genome of an organism remains non-trivial. In this study, we present the draft genome of the black grouse, wh…
Review of Non-English Corpora Annotated for Emotion Classification in Text
2020
In this paper we try to systematize the information about the available corpora for emotion classification in text for languages other than English with the goal to find what approaches could be used for low-resource languages with close to no existing works in the field. We analyze the corresponding volume, emotion classification schema, language of each corresponding corpus and methods employed for data preparation and annotation automation. We’ve systematized twenty-four papers representing the corpora and found that corpora were mostly for the most spoken world languages: Hindi, Chinese, Turkish, Arabic, Japanese etc. A typical corpus contained several thousand of manually-annotated ent…
Annotation of microsporidian genomes using transcriptional signals
2012
EA GenoSol CT3; International audience; High-quality annotation of microsporidian genomes is essential for understanding the biological processes that govern the development of these parasites. Here we present an improved structural annotation method using transcriptional DNA signals. We apply this method to re-annotate four previously annotated genomes, which allow us to detect annotation errors and identify a significant number of unpredicted genes. We then annotate the newly sequenced genome of Anncaliia algerae. A comparative genomic analysis of A. algerae permits the identification of not only microsporidian core genes, but also potentially highly expressed genes encoding membrane-asso…
The evolution of splicing: transcriptome complexity and transcript distances implemented in TranD
2021
AbstractAlternative splicing contributes to organismal complexity. Comparing transcripts between and within species is an important first step toward understanding questions about how evolution of transcript structure changes between species and contributes to sub-functionalization. These questions are confounded with issues of data quality and availability. The recent explosion of affordable long read sequencing of mRNA has considerably widened the ability to study transcriptional variation in non-model species. In this work, we develop a computational framework that uses nucleotide resolution distance metrics to compare transcript models for structural phenotypes: total transcript length,…