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ParsEval: parallel comparison and analysis of gene structure annotations

Daniel S Standage, Volker P Brendel
2012 BMC Bioinformatics  
We developed ParsEval, a software application for pairwise comparison of sets of gene structure annotations.  ...  We developed ParsEval, a software application for pairwise comparison of sets of gene structure annotations.  ...  Acknowledgements The authors would like to thank the developers of the GenomeTools software for helpful feedback regarding integration of AnnotationSketch and our colleagues Drs.  ... 
doi:10.1186/1471-2105-13-187 pmid:22852583 pmcid:PMC3439248 fatcat:ufm77ghg3fh63ny66pidtzrwmi

xGDBvm: A Web GUI-driven workflow for annotating eukaryotic genomes in the cloud

Jon Duvick, Daniel S Standage, Nirav Merchant, Volker P Brendel
2016 The Plant Cell  
Genome-wide annotation of gene structure requires the integration of numerous computational steps.  ...  To address this problem, we developed the xGDBvm software, which uses an intuitive graphical user interface to access a number of common genome analysis and gene structure tools, preconfigured in a self-contained  ...  Comparison of 19,892 loci with gene models from both CpGAT and the published annotation using ParsEval (Standage and Brendel, 2012 ) revealed a high level of congruence between the two data sets.  ... 
doi:10.1105/tpc.15.00933 pmid:27020957 pmcid:PMC4863385 fatcat:yxvpcrvys5g6hcmyirzjbswu54

PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity

Andrei Rozanski, HongKee Moon, Holger Brandl, José M Martín-Durán, Markus A Grohme, Katja Hüttner, Kerstin Bartscherer, Ian Henry, Jochen C Rink
2018 Nucleic Acids Research  
At its core, PlanMine continues to utilize the powerful InterMine framework and consistent data annotations to enable meaningful inter-species comparisons.  ...  The addition of recent single cell and bulk RNA-seq datasets greatly expands the available gene expression information.  ...  in parallel.  ... 
doi:10.1093/nar/gky1070 pmid:30496475 fatcat:vgpg4jdqlvfx3fi3uofgivhdky

PacBio assembly of a Plasmodium knowlesi genome sequence with Hi-C correction and manual annotation of the SICAvar gene family

S. A. LAPP, J. A. GERALDO, J.-T. CHIEN, F. AY, S. B. PAKALA, G. BATUGEDARA, J. HUMPHREY, J. D. DeBARRY, K. G. Le ROCH, M. R. GALINSKI, J. C. KISSINGER
2017 Parasitology  
This sequence and annotation, referred to as the 'MaHPIC Pk genome sequence', includes manual annotation of the SICAvar gene family with 136 full-length members categorized as type I or II.  ...  This sequence provides a framework that will permit a better understanding of the SICAvar repertoire, selective pressures acting on this gene family and mechanisms of antigenic variation in this species  ...  To evaluate the gene models produced by the MAKER2 and Companion approaches, a comparison between both annotations was performed using ParsEval (Standage and Brendel, 2012) .  ... 
doi:10.1017/s0031182017001329 pmid:28720171 pmcid:PMC5798397 fatcat:oe6smag7pbbrhc44nvae4odpbi

Survey on index based homology search algorithms

Xianyang Jiang, Peiheng Zhang, Xinchun Liu, Stephen S.-T. Yau
2007 Journal of Supercomputing  
Up to now, there are many homology search algorithms that have been investigated and studied. However, a good classification method and a comprehensive comparison for these algorithms are absent.  ...  Based on the classification, the characteristics of the currently popular index based homology search algorithms are compared and analyzed.  ...  The authors thank Professor Dominique Lavenier for his valuable suggestions on this paper, and also thank anonymous reviewers for their comments to improve the readability of this paper.  ... 
doi:10.1007/s11227-006-0041-0 fatcat:hhijz2rah5a5jcbu4d6ecj3npi

Density-Connected Subspace Clustering for High-Dimensional Data [chapter]

Karin Kailing, Hans-Peter Kriegel, Peer Kröger
2004 Proceedings of the 2004 SIAM International Conference on Data Mining  
Several application domains such as molecular biology and geography produce a tremendous amount of data which can no longer be managed without the help of efficient and effective data mining methods.  ...  In contrast to existing grid-based approaches, SUBCLU is able to detect arbitrarily shaped and positioned clusters in subspaces.  ...  Acknowledgments We want to acknowledge the work of Alexandra Boshammer and Elke Schumm supporting the implementation of SUBCLU and CLIQUE, respectively.  ... 
doi:10.1137/1.9781611972740.23 dblp:conf/sdm/KroegerKK04 fatcat:ys4fwxrtrnh4jcfuvqbw3glxdi

Definition and variation of human endogenous retrovirus H

Patric Jern, Göran O. Sperber, Jonas Blomberg
2004 Virology  
A pattern of abundant defective elements and less abundant less defective ones led us to formulate a bmidwifeQ master model where more complete elements help the others in trans to transpose.  ...  The HERV-H group was divided into RTVLH2-like (705 elements) and RGH2-like (77 elements) subgroups.  ...  Acknowledgments We thank Tove Airola for help in data collection and Dmitrij Uzameckis for providing DNA samples for the TGGE.  ... 
doi:10.1016/j.virol.2004.06.023 pmid:15327901 fatcat:w23xzcdcircmdg6yufze4ap4ju

The ABCE1 capsid assembly pathway is conserved between primate lentiviruses and the non-primate lentivirus feline immunodeficiency virus [article]

Jonathan C. Reed, Nick Westergreen, Brook C. Barajas, Dylan Ressler, Daryl J. Phuong, John V. Swain, Vishwanath R. Lingappa, Jaisri R. Lingappa
2017 bioRxiv   pre-print
First, we found that, unlike for HIV-1, the FIV completed immature capsid and the largest putative assembly intermediate are unstable during analysis.  ...  During immature capsid assembly in cells, the Gag protein of HIV-1 and other primate lentiviruses co-opts a host RNA granule, forming a pathway of assembly intermediates that contains host components,  ...  No reuse allowed without permission. 719 720 Structure 720 Alignment and Sequence Analysis.  ... 
doi:10.1101/183848 fatcat:zkbnu6pzg5a5jcztnnmajcubai

A Novel Approach for Acoustic Signal Processing of a Drum Shearer based on Improved Variational Mode Decomposition and Cluster Analysis

Changpeng Li, Tianhao Peng, Yanmin Zhu
2020 Sensors  
The PSO was designed to optimize the clustering analysis, and the minimum envelope entropy of the acoustic signal was regarded as the feature for classification.  ...  According to the results, the approach determined the number of modes and penalty parameters for VMD. Then the improved VMD algorithm decomposed the acoustic signal.  ...  Acknowledgments: The support of the National Natural Science Foundation of China (No. 51475001). Conflicts of Interest: The authors declare no conflicts of interest.  ... 
doi:10.3390/s20102949 pmid:32456034 pmcid:PMC7288331 fatcat:4absnclyovddjidz4hjw5rsghi

Divide or unite—a novel molecular switch in endometrial carcinoma

Martin Götte
2006 Journal of Molecular Medicine  
Zhiwei Wu (School of Dental Medicine, University of Pennsylvania) for his critical comments and grammatical correction of the manuscript.  ...  Acknowledgements Support: NIH research grants to MEA (HL062494, HL70250, and HL46681) and RJC (MH63232). MEA is an AHA-established Investigator.  ...  While Koch's postulates for infectious disease do not provide a completely parallel analysis for the study of structural heart disease, it is becoming increasingly clear that CaMKII is a critical cardiomyopathic  ... 
doi:10.1007/s00109-006-0118-5 pmid:17068656 fatcat:ppo4q2a4n5bsnje234omgfubi4

The Stanford typed dependencies representation

Marie-Catherine de Marneffe, Christopher D. Manning
2008 Coling 2008: Proceedings of the workshop on Cross-Framework and Cross-Domain Parser Evaluation - CrossParser '08   unpublished
We consider the underlying design principles of the Stanford scheme from this perspective, and compare it to the GR and PARC representations.  ...  Finally, we address the question of the suitability of the Stanford scheme for parser evaluation.  ...  Acknowledgments We wish to thank Andrew Brian Clegg and Sampo Pyysalo for their useful feedback on the dependency extraction tool. Their comments enabled us to improve the tool.  ... 
doi:10.3115/1608858.1608859 fatcat:mnrgpr74f5avxezbtbqti6nnoi

Acoustics of ancient Greek and Roman theaters in use today

Anders Christian Gade, Konstantinos Angelakis
2006 Journal of the Acoustical Society of America  
inverse filter of the common harmonic structure on specmurt analysis are discussed.  ...  Inverse filter analysis of common harmonic structure on Specmurt using Riemann's function. Nobutaka Ono, Shoichiro Saito, Hirokazu Kameoka, and Shigeki Sagayama ͑Dept.  ...  property and structure of the bottom.  ... 
doi:10.1121/1.4787803 fatcat:3lczeegofreblpjmfixt7gdxv4

Human genome interaction: models for designing DNA sequences [article]

Emily Alice Scher, University Of Edinburgh, Guido Sanguinetti, Shay Cohen
2021
Instead of limiting themselves to simple genetic circuits, researchers aim for genome-scale organism redesigns, revolutionary gene therapies, and high throughput, industrial scale natural product syntheses  ...  A tool called Part Crafter (partcrafter.com) will be presented, which aggregates sequence and annotation data from a variety of data sources to allow for rational search over genomic features, as well  ...  A tree of nonterminals was built for each gene in the human genome based on the structure of the annotated features it contains.  ... 
doi:10.7488/era/812 fatcat:6zzvikmoinfg5iu2wjs3zx2nfi

New Techniques for Clustering Complex Objects

Karin Kailing, Hans-Peter Kriegel
2004 unpublished
We begin our analysis with the assumption of no index structure.  ...  Since some genes have missing expression values and the handling of missing values in gene expression analysis is a non-trivial task, we eliminated those genes from our test data set.  ... 
fatcat:7ilttjrlxrbvbjn27vcft4mvzi

Drug targets of the heartworm, "Dirofilaria immitis"

Christelle Godel, Pascal Mäser, Ronald Kaminsky, Jürg Utzinger
2012 unpublished
from the University of Edinburgh for their help to share their knowledge and success in bioinformatics as well as their huge education concerning nematode parasites to set a good publication.  ...  Novartis Animal Health St-Aubin FR and the Swiss Tropical and Public Health Institute to allow me to perform my PhD and share the results and interesting data with relevant persons and for the fellowship  ...  Acknowledgments We thank Claudio and Marco Genchi for providing D. immitis from Pavia and Andrew Moorhead for the D. immitis from Athens, GA.  ... 
doi:10.5451/unibas-006021331 fatcat:uvp4s7ofsfbwdkj5d46n6v4yay
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