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ParsEval: parallel comparison and analysis of gene structure annotations

Daniel S Standage, Volker P Brendel
2012 BMC Bioinformatics  
Accurate gene structure annotation is a fundamental but somewhat elusive goal of genome projects, as witnessed by the fact that (model) genomes typically undergo several cycles of re-annotation. In many cases, it is not only different versions of annotations that need to be compared but also different sources of annotation of the same genome, derived from distinct gene prediction workflows. Such comparisons are of interest to annotation providers, prediction software developers, and end-users,
more » ... ho all need to assess what is common and what is different among distinct annotation sources. We developed ParsEval, a software application for pairwise comparison of sets of gene structure annotations. ParsEval calculates several statistics that highlight the similarities and differences between the two sets of annotations provided. These statistics are presented in an aggregate summary report, with additional details provided as individual reports specific to nonoverlapping, gene-model-centric genomic loci. Genome browser styled graphics embedded in these reports help visualize the genomic context of the annotations. Output from ParsEval is both easily read and parsed, enabling systematic identification of problematic gene models for subsequent focused analysis. Results ParsEval is capable of analyzing annotations for large eukaryotic genomes on typical desktop or laptop hardware. In comparison to existing methods, ParsEval exhibits a considerable performance improvement, both in terms of runtime and memory consumption. Reports from ParsEval can provide relevant biological insights into the gene structure annotations being compared. Conclusions Implemented in C, ParsEval provides the quickest and most feature-rich solution for genome annotation comparison to date. The source code is freely available (under an ISC license) at Abstract Background: Accurate gene structure annotation is a fundamental but somewhat elusive goal of genome projects, as witnessed by the fact that (model) genomes typically undergo several cycles of re-annotation. In many cases, it is not only different versions of annotations that need to be compared but also different sources of annotation of the same genome, derived from distinct gene prediction workflows. Such comparisons are of interest to annotation providers, prediction software developers, and end-users, who all need to assess what is common and what is different among distinct annotation sources. We developed ParsEval, a software application for pairwise comparison of sets of gene structure annotations. ParsEval calculates several statistics that highlight the similarities and differences between the two sets of annotations provided. These statistics are presented in an aggregate summary report, with additional details provided as individual reports specific to non-overlapping, gene-model-centric genomic loci. Genome browser styled graphics embedded in these reports help visualize the genomic context of the annotations. Output from ParsEval is both easily read and parsed, enabling systematic identification of problematic gene models for subsequent focused analysis. Results: ParsEval is capable of analyzing annotations for large eukaryotic genomes on typical desktop or laptop hardware. In comparison to existing methods, ParsEval exhibits a considerable performance improvement, both in terms of runtime and memory consumption. Reports from ParsEval can provide relevant biological insights into the gene structure annotations being compared. Conclusions: Implemented in C, ParsEval provides the quickest and most feature-rich solution for genome annotation comparison to date. The source code is freely available (under an ISC license) at http://parseval.sourceforge.net/.
doi:10.1186/1471-2105-13-187 pmid:22852583 pmcid:PMC3439248 fatcat:ufm77ghg3fh63ny66pidtzrwmi

Kevlar: a mapping-free framework for accurate discovery of de novo variants [article]

Daniel S Standage, C Titus Brown, Fereydoun Hormozdiari
2019 bioRxiv   pre-print
Thus, we formally define the score assigned to each variant for being de novo as S L = log L(dn = 1) − max{log(L(ih = 1)), log(L(f p = 1))}.  ... 
doi:10.1101/549154 fatcat:fqicqb6mize77crgvn7ynnd7i4

MicroHapDB: a portable and extensible database of all published microhaplotype marker and frequency data [article]

Daniel S Standage, Rebecca N Mitchell
2020 bioRxiv   pre-print
Standage & Mitchell between markers or adopting an either/or strategy in which one of the loci is discarded when both produce  ...  populations and then averaged In float the marker's informativeness for assignment (I n ) for 26 global populations Source string the source from which this marker definition was obtained Standage  ... 
doi:10.1101/2020.04.08.032052 fatcat:fnij3k6jsvhsbmbt5qmsx3wgl4

iLoci: Robust evaluation of genome content and organization for provisional and mature genome assemblies [article]

Daniel S Standage, Tim Lai, Volker P Brendel
2021 bioRxiv   pre-print
Operational definition of iLoci Basic procedure Computing iLoci for an assembled contig/scaffold/pseudo-chromosome S depends on a set of intervals G (corresponding to gene models annotated on S) and  ...  Such values can then be attached to an iLocus annotation using key-value pairs in GFF3's attribute column.  ... 
doi:10.1101/2021.10.03.462917 fatcat:lg6ru2er6fbuxjciarpykkygsy

Kevlar: a mapping-free framework for accurate discovery of de novo variants

Daniel S. Standage, C. Titus Brown, Fereydoun Hormozdiari
2019 iScience  
Thus, we formally define the score assigned to each variant for being de novo as S L = log L(dn = 1) − max{log(L(ih = 1)), log(L(f p = 1))}.  ...  Standage, C. Titus Brown, and Fereydoun Hormozdiari Supplemental Information Kevlar: a mapping-free framework for accurate discovery of de novo variants Daniel S. Standage, C.  ...  S.  ... 
doi:10.1016/j.isci.2019.07.032 pmid:31377530 pmcid:PMC6682328 fatcat:znvfzlo2tvb7rnuc35xiliq4oe

MicroHapDB: A Portable and Extensible Database of All Published Microhaplotype Marker and Frequency Data

Daniel S. Standage, Rebecca N. Mitchell
2020 Frontiers in Genetics  
HSHQDC-15-C-00064 awarded to Battelle National Biodefense Institute by the Department of Homeland Security Science and Technology Directorate (DHS S&T) for the management and operation of the National  ...  amplification), correct interpretation of DNA profiles requires researchers to determine the independence of markers in a proposed panel based on the extent of linkage between the markers in the population(s)  ... 
doi:10.3389/fgene.2020.00781 pmid:32849792 pmcid:PMC7427474 fatcat:tht24avf65hg5iytcjuprhxqja

TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction

Erin L. Doyle, Nicholas J. Booher, Daniel S. Standage, Daniel F. Voytas, Volker P. Brendel, John K. VanDyk, Adam J. Bogdanove
2012 Nucleic Acids Research  
Users enter their sequence(s) in a text box or upload a file containing the sequence(s). Allowable file size is up to 2 MB.  ...  By default, the tool searches only the sequence(s) as entered; a checkbox option includes also the reverse complement sequence(s).  ... 
doi:10.1093/nar/gks608 pmid:22693217 pmcid:PMC3394250 fatcat:wqho65z4bvffta3if25epqqnxm

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  
The user sets an "Update" flag on the configuration page, specifies a directory where update data resides, and selects the data type(s) and update action(s) desired.  ...  Users can also upload precomputed genome annotations provided as GFF3 file(s) along with optional transcript and translation FASTA files.  ... 
doi:10.1105/tpc.15.00933 pmid:27020957 pmcid:PMC4863385 fatcat:yxvpcrvys5g6hcmyirzjbswu54

Genome, transcriptome and methylome sequencing of a primitively eusocial wasp reveal a greatly reduced DNA methylation system in a social insect

Daniel S. Standage, Ali J. Berens, Karl M. Glastad, Andrew J. Severin, Volker P. Brendel, Amy L. Toth
2016 Molecular Ecology  
Gibson; P. dominula by S. McCann; S. invicta and Apis mellifera by A. Wild.  ...  Toth, S. Sankaranarayanan and V. P. Brendel, in preparation).  ... 
doi:10.1111/mec.13578 pmid:26859767 fatcat:t24fux2d5ndhhpifstfuc6cduq

Konzepte und Maßnahmen zum Umgang mit soziotechnischen Herausforderungen bei der Entsorgung radioaktiver Abfälle [chapter]

Achim Brunnengräber, Ana María Isidoro Losada, Bettina Brohmann, Peter Hocke
2021 Robuste Langzeit-Governance bei der Endlagersuche  
Mit dem Atomausstieg, der in Deutschland bis Ende 2022 vollzogen sein soll, dem Standortauswahlgesetzt (StandAG 2013, geändert in 2017) und der Arbeit der Endlagerkommission (2014-2016) sowie der darauffolgenden  ...  Der Gesetzgeber hat sich im StandAG mit der Begriffsbestimmung in § 1 Abs. 5 S. 1 und nach Maßgabe der § § 12ff. für eine ganz bestimmte Ausgestaltung von Reversibilität entschieden -die Festlegung des  ...  Auch das StandAG 2017 -und nicht nur das StandAG 2013 -ist auf Fortentwicklung angelegt.  ... 
doi:10.14361/9783839456682-002 fatcat:ds7tq5yt7bd4riz32xtimi426u

Konfrontation, Kooperation oder Kooptation

Achim Brunnengräber, Felix Syrovatka
2016 Prokla  
I S . 2553), zuletzt geändert durch die Verordnung vom 31 . August 2015 (BGBl .  ...  1 Wir danken Tobias Haas, Daniel Häfner und der PROKLA-Redaktion für die hilfreichen Anmerkungen und Kommentare zu den vorhergehenden Versionen unseres Textes . 2 Als Anti-Atom-oder Anti-AKW-Bewegung sollen  ... 
doi:10.32387/prokla.v46i184.121 fatcat:g7p62mwuuvf7rol6xighihwz4q

Page 1531 of Psychological Abstracts Vol. 61, Issue 6 [page]

1979 Psychological Abstracts  
, Linda S., 12632 Salazar, Jaime G., 13241 Salinas, Manvel, 14236 Sall, Gary S., 12248 Salthouse, Timothy A., 12514, 12650 Saltzberg, Lee S., 14547 Salzano, F.  ...  R., 12453 Schindler, Robert M., 12583 Schindler, Ulrich, 14641 Schipper, Lowell M., 12568 Schiraldi, Frank R., 14364 Schlaffer, Edit, 13303 Schleifer, Lawrence M., 13874 Schlosky, Daniel P., 13058 Schlossman  ... 

Page 4060 of Psychological Abstracts Vol. 79, Issue 9 [page]

1992 Psychological Abstracts  
N., 30396 Solano, Cecilia H., 30797 Soliday, Jill, 33417 Solomo: Solomon, Gary S., "29754 Solorzano, Daniel G., 33142 Soiowczuk, Kathleen A., 30606 Somat, Alain, 31114 Somers, Anne eg 32687 Somers, Marcia  ...  33465 Stacy, Alan W., 30827 Stadter, Richard, 31984 Stafford, Mark C., 31588 Stairs, Arlene, 45 Stajic, Marina, 31651 Stalker, Carol A., 32258 Stallone, Daryth D., 30397 Stamenkovic-Radak, Marina, 30224 Standage  ... 

Page 4510 of Psychological Abstracts Vol. 87, Issue 11 [page]

2000 Psychological Abstracts  
S.. 31713 Stamper, Ewa, 33269 Stancampiano, Roberto, 32189 Standage, Kevin, 33197 Stangier, Ulrich, 33492 Stanley, Jason, 32495, 32496 Stanley, Melinda A., 33183 Stanton, J. M., 34687 Stanton, N.  ...  D., 31754 Smith, Christopher M., 33666 Smith, Daniel W., 33329 Smith, Deborah. 34186 Smith, Eric Alden, 32746 Smith.  ... 

Page 75 of Problems in General Surgery Vol. 16, Issue 4 [page]

1999 Problems in General Surgery  
Quinn SF, Schuman SF, Demlow TA, Standage BA, Ragsdale JW, Green GS, Sheley RC.  ...  Hoffer EK, Sultan S, Herskowitz MM, Daniels ID, Sclafani SJ. Prospective randomized trial of a metallic intravascular stent in hemodialysis graft maintenance. J Vasc Interv Radiol 1997;8:965-73. .  ... 
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