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Compositional features of eukaryotic genomes for checking predicted genes

S. Cruveiller
2003 Briefings in Bioinformatics  
Acknowledgments We thank Adam Pavlícek for helpful discussions and references and for communicating results prior to publication. We also thank an anonymous referee for valuable suggestions.  ...  both of them show similar compositional anomalies for a large proportion of the predicted genes.  ...  Finally, it should be mentioned that compositional approaches can be useful also for visualising, comparing and checking draft genome assemblies (contig order and orientation).  ... 
doi:10.1093/bib/4.1.43 pmid:12715833 fatcat:dqadqwtuvjg7hcqbuqe6btmt6y

Arabidopsis genome analysis as exemplified by analysis of chromosome 4

K. F.X. Mayer
2000 Briefings in Bioinformatics  
Beside an overview on methods and strategies for Arabidopsis genome analysis, a summary of the results from the first analysis is presented.  ...  During the last decade the small cruciferous plant Arabidopsis thaliana has become a model organism for flowering plants. Sequencing and analysis of the Arabidopsis genome is nearing completion.  ...  gene finding in higher eukaryotes involves the modelling of complete genes from the combination of predicted introns, exons and splice sites.  ... 
doi:10.1093/bib/1.4.389 pmid:11465056 fatcat:df4gtvodtrgalpacjyn3gzfgxm

EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems

Valerie Eichinger, Thomas Nussbaumer, Alexander Platzer, Marc-André Jehl, Roland Arnold, Thomas Rattei
2015 Nucleic Acids Research  
EffectiveDB contains pre-calculated predictions for currently 1677 bacterial genomes from the EggNOG 4.0 database and for additional bacterial genomes from NCBI RefSeq.  ...  Here we describe a major update of the database, which was previously featured in the NAR Database Issue.  ...  For any usersubmitted FASTA file an optional check of genome completeness by CheckM  ... 
doi:10.1093/nar/gkv1269 pmid:26590402 pmcid:PMC4702896 fatcat:pelisaa7kbcszhox3twitoyqua

Computational Approaches for Transcription Factor Binding Prediction

Smitha CS, Saritha R
2014 International Journal of Computer Applications  
In this paper a detailed survey of some of the prediction approaches in both prokaryotes and eukaryotes have been made.  ...  The prediction results may be useful for identification of putative binding sites.  ...  A portion of the genome called gene is the basic unit of carrier. The genome is packed in chromosomes within the nucleus of a cell.  ... 
doi:10.5120/16384-5969 fatcat:36euotnhqrfeppamf52mqeglrm

Large Scale Sequencing and Analysis of AT Rich Eukaryote Genomes

Gernot Glockner
2000 Current Genomics  
Additionally, the currently available analysis tools are mainly suitable for gene finding in genomes with normal base composition.  ...  Techniques designed for large scale sequencing and assembly of genomes with normal base composition will fail with these unusual genomes.  ...  In (Table 1 ) the genomic features of selected lower eukaryote genomes with very high AT content, and for which a reasonable number of sequence data is available, are summarised.  ... 
doi:10.2174/1389202003351472 fatcat:vttz65id4veljjt5m4v35chw7m

EuPaGDT: a web tool tailored to design CRISPR guide RNAs for eukaryotic pathogens

Duo Peng, Rick Tarleton
2015 Microbial Genomics  
Flexibility in gRNA design, accommodating unique eukaryotic pathogen (gene and genome) attributes and high-throughput gRNA design are the main features that distinguish EuPaGDT from other gRNA design tools  ...  Recent development of CRISPR-Cas9 genome editing has enabled highly efficient and versatile manipulation of a variety of organisms and adaptation of the CRISPR-Cas9 system to eukaryotic pathogens has opened  ...  Acknowledgements We thank Dave Dowless for technical assistance with setting up the webserver hosting EuPaGDT.  ... 
doi:10.1099/mgen.0.000033 pmid:28348817 pmcid:PMC5320623 fatcat:xqef2g5zizhbllykwekxaicgsq

Complex archaea that bridge the gap between prokaryotes and eukaryotes

Anja Spang, Jimmy H. Saw, Steffen L. Jørgensen, Katarzyna Zaremba-Niedzwiedzka, Joran Martijn, Anders E. Lind, Roel van Eijk, Christa Schleper, Lionel Guy, Thijs J. G. Ettema
2015 Nature  
During the early stages of the genomic era, it also became apparent that eukaryotic genomes were chimaeric by nature 8,9 , comprising genes of both archaeal and bacterial origin, in addition to genes specific  ...  Ever since the recognition of the archaeal domain of life by Carl Woese and co-workers 4,5 , Archaea have featured prominently in hypotheses for the origin of eukaryotes, as eukaryotes and Archaea represented  ...  Acknowledgements We dedicate this paper to the memory of Rolf Bernander. We thank P. Offre and I. de Bruijn for technical advice and useful discussions, and A. Denny for image processing.  ... 
doi:10.1038/nature14447 pmid:25945739 pmcid:PMC4444528 fatcat:tjlqdt3awjh5fgiewjns347ayi

Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features

Shiva Kumar, Faraz A Ansari, Vinod Scaria
2009 Virology Journal  
MicroRNAs (small ~22 nucleotide long non-coding endogenous RNAs) have recently attracted immense attention as critical regulators of gene expression in multi-cellular eukaryotes, especially in humans.  ...  However, most of these widely used tools are dependent on structural features and sequence conservation which limits their use in discovering novel virus expressed microRNAs and non-conserved eukaryotic  ...  This work was funded by the Council for Scientific and Industrial Research (CSIR), India through project: "Comparative Genomics and Biology of Non-coding RNA" (NWP0036).  ... 
doi:10.1186/1743-422x-6-129 pmid:19691855 pmcid:PMC2743665 fatcat:h76hxa5jbjfufge77dikcourfi

Measures of Compositional Strand Bias Related to Replication Machinery and its Applications

Kazuharu Arakawa, Masaru Tomita
2012 Current Genomics  
Such strand bias in genomes, frequently visualized by GC skew graphs, is used for the computational prediction of transcription start sites and replication origins, as well as for comparative evolutionary  ...  Here, we review the measures of strand bias that have been proposed to date, including the GC skew, the B 1 index, the predictability score of linear discriminant analysis for gene orientation, the signal-to-noise  ...  The Predictability Score of Linear Discriminant Analysis of Gene Orientation Nucleotide compositional skews often coincide with gene orientation skews [25, 67] .  ... 
doi:10.2174/138920212799034749 pmid:22942671 pmcid:PMC3269016 fatcat:f675oeebyzgzdm5nks7ci3z3cy

Widespread of horizontal gene transfer in the human genome

Wenze Huang, Lillian Tsai, Yulong Li, Nan Hua, Chen Sun, Chaochun Wei
2017 BMC Genomics  
Horizontal gene transfer has been found prevalent in prokaryotes but very rare in eukaryote. In this paper, we investigate horizontal gene transfer in the human genome.  ...  An alternative mechanism of gene acquisition is through horizontal gene transfer (HGT), which involves movement of genetic materials between different species.  ...  All scripts for this paper have been deposited into Github at HGT-in-Human-Genome and are freely available to all users.  ... 
doi:10.1186/s12864-017-3649-y pmid:28376762 pmcid:PMC5379729 fatcat:4pvi3jvxk5e2zeluael66v5rte

GeneExpress: a computer system for description, analysis, and recognition of regulatory sequences in eukaryotic genome

N A Kolchanov, M P Ponomarenko, A E Kel, Kondrakhin YuV, A S Frolov, F A Kolpakov, T N Goryachkovsky, O V Kel, E A Ananko, E V Ignatieva, O A Podkolodnaya, V N Babenko (+13 others)
1998 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
and contextual features of mRNA 5'UTRs and prediction of their translation efficiency; and (5) ACTIVITY is the module for analysis and site activity prediction of a given nucleotide sequence.  ...  and visualization of the GeneNet information; (2) Transcription Regulation combines the database on transcription regulatory regions of eukaryotic genes (TRRD) and TRRD Viewer; (3) Transcription Factor  ...  Acknowledgments This work was supported partially by grants of Russian National Human Genome Project, Russian Ministry of Science and Technical Politics, Siberian Department of Russian Academy of Sciences  ... 
pmid:9783214 fatcat:dgjqc755gve2ljpxqpn45hfc74

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes

G. Parra, K. Bradnam, I. Korf
2007 Bioinformatics  
Motivation: The numbers of finished and ongoing genome projects are increasing at a rapid rate, and providing the catalog of genes for these new genomes is a key challenge.  ...  Results: In this study, we report a computational method, CEGMA (Core Eukaryotic Genes Mapping Approach), for building a highly reliable set of gene annotations in the absence of experimental data.  ...  Funding to pay the Open Access charges was provided by NHGRI (National Human Genome Research Institute). Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btm071 pmid:17332020 fatcat:vzo5lx3gonfa3egti2o7nnfjuu

Missing Genes, Multiple ORFs, and C-to-U Type RNA Editing in Acrasis kona (Heterolobosea, Excavata) Mitochondrial DNA

Cheng-Jie Fu, Sanea Sheikh, Wei Miao, Siv G.E. Andersson, Sandra L. Baldauf
2014 Genome Biology and Evolution  
Discoba (Excavata) is an ancient group of eukaryotes with great morphological and ecological diversity.  ...  We have assembled a complete mtDNA genome from the aggregating heterolobosean amoeba, Acrasis kona, which consists of a single circular highly ATrich (83.3%) molecule of 51.5 kb.  ...  Spiegel (University of Arkansas)  ... 
doi:10.1093/gbe/evu180 pmid:25146648 pmcid:PMC4202320 fatcat:jblpwmhgxff2jhlac7vdiaei5u

Recognition of Protein-coding Genes Based on Z-curve Algorithms

Feng-Biao Guo, Yan Lin, Ling-Ling Chen
2014 Current Genomics  
Recognition of protein-coding genes, a classical bioinformatics issue, is an absolutely needed step for annotating newly sequenced genomes.  ...  ZCURVE_C (for 57 bacteria) and Zfisher (for any bacterium) are web servers for re-annotation of bacterial and archaeal genomes.  ...  This study was supported by the program for New Century Excellent Talents in University (grant NCET-11-0059), the National Natural Science Foundation of China (grants 31071109, 31071659, 31271406).  ... 
doi:10.2174/1389202915999140328162724 pmid:24822027 pmcid:PMC4009845 fatcat:lpvjmkh5yvd2zc2mb3obeonisi

Deducing Intracellular Distributions of Metabolic Pathways from Genomic Data [chapter]

Ansgar Gruber, Peter G. Kroth
2013 Msphere  
This is partially because sequencing, assembly, and au mmatcd at>no~tion can be done much fuster than the identification, classification, and prediction oftl>c intracellular localization of the gene products  ...  Additionally, we describe Stralcgies suitable for those groups of algae with secondary plastids (for instance dia1oms), which arc characterized by a different cellulu topology and a larger number of intracellular  ...  Acknowledgements References The authors are grateful for helpful discussions wim Daniela Ewe and for financial support by the German Research Foundation (DFG) to PGK (KRl661/3-4 and SFB969, project A04  ... 
doi:10.1007/978-1-62703-661-0_12 pmid:24218217 fatcat:qwl2rdald5g6rpg6yvy37vwcgy
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