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Structural and Functional Annotation of Eukaryotic Genomes with GenSAS [chapter]

Jodi L. Humann, Taein Lee, Stephen Ficklin, Dorrie Main
2019 Msphere  
The Genome Sequence Annotation Server (GenSAS, https://www.gensas.org) is a secure, web-based genome annotation platform for structural and functional annotation, as well as manual curation.  ...  Requiring no installation by users, GenSAS integrates popular command line-based, annotation tools under a single, easy-to-use, online interface.  ...  We also acknowledge the WSU Hort 550 (Bioinformatics for Research) graduate classes of 2015, 2016, and 2017 for testing and providing feedback about GenSAS.  ... 
doi:10.1007/978-1-4939-9173-0_3 fatcat:zhg237hfxbdjrnaebg7lvsjfia

Uniform standards for genome databases in forest and fruit trees

J. L. Wegrzyn, D. Main, B. Figueroa, M. Choi, J. Yu, D. B. Neale, S. Jung, T. Lee, M. Stanton, P. Zheng, S. Ficklin, I. Cho (+8 others)
2012 Tree Genetics & Genomes  
This is achieved through focused development on data input standards (templates), pipelines for the storage and automated curation, and consistent annotation efforts through the application of widely accepted  ...  Efforts towards standardization are not limited to genotype/phenotype experiments but are also being applied to other data types to improve gene prediction and annotation for de novo sequencing projects  ...  One of the first objectives under this project will be the integration of a web-based annotation tool known as the Genome Sequence Annotation Server (GenSAS) which is being developed to provide fruit tree  ... 
doi:10.1007/s11295-012-0494-7 fatcat:uvc6tk3mf5bzjbmqmkb6an3zqi

Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing

Girum Fitihamlak Ejigu, Jaehee Jung
2020 Biology  
Next-Generation Sequencing (NGS) has made it easier to obtain genome-wide sequence data and it has shifted the research focus into genome annotation.  ...  Here, we present a summary of both structural and functional annotations, as well as the associated comparative annotation tools and pipelines.  ...  Genome Sequence Annotation Serve (GenSAS) [133] is an online pipeline that provides both structural and functional annotations for eukaryotic and prokaryotic genomes.  ... 
doi:10.3390/biology9090295 pmid:32962098 pmcid:PMC7565776 fatcat:gdaxbwygqnaapiqisyf56ajpea

FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow

Anna Vlasova, Toni Hermoso Pulido, Francisco Camara, Julia Ponomarenko, Roderic Guigó
2021 Genes  
Functional annotation allows adding biologically relevant information to predicted features in genomic sequences, and it is, therefore, an important procedure of any de novo genome sequencing project.  ...  The pipeline integrates different annotation approaches, such as NCBI BLAST+, DIAMOND, InterProScan, and KEGG.  ...  Acknowledgments: We would like to thank Paolo di Tommaso of Seqera Labs (formerly of CRG) for his advice on setting up the pipeline into the Nextflow framework.  ... 
doi:10.3390/genes12101645 pmid:34681040 pmcid:PMC8535801 fatcat:4msl357xwfbp5luo6cccm6cabi

Apollo: Democratizing genome annotation [article]

Nathan Dunn, Deepak Unni, Colin Diesh, Monica Munoz-Torres, Nomi Harris, Eric Yao, Helena Rasche, Ian Holmes, Christine Elsik, Suzanna Lewis
2019 bioRxiv   pre-print
Its technical architecture enables Apollo to be integrated into multiple existing genomic analysis pipelines and heterogeneous laboratory workflow platforms.  ...  Genome annotation is the process of identifying the location and function of a genome's encoded features.  ...  Acknowledgements Thanks to the Apollo and JBrowse communities for bringing issues to our attention, requesting new features, contributing code, integrating and using our product.  ... 
doi:10.1101/512376 fatcat:vnyf6dwbrfecrj5s6vh7psxfli

Twelve quick steps for genome assembly and annotation in the classroom

Hyungtaek Jung, Tomer Ventura, J. Sook Chung, Woo-Jin Kim, Bo-Hye Nam, Hee Jeong Kong, Young-Ok Kim, Min-Seung Jeon, Seong-il Eyun, Francis Ouellette
2020 PLoS Computational Biology  
In genomics, generating a high-quality genome assembly/annotation has become an indispensable tool for better understanding the biology of any species.  ...  Indeed, selecting the most appropriate sequencing and software platforms and annotation pipelines for a new genome project can be daunting because tools often only work in limited contexts.  ...  GenSAS https://www.gensas.org Integrates with JBrowse and Apollo. An automatic platform and pipeline for genome structural and functional annotation.  ... 
doi:10.1371/journal.pcbi.1008325 pmid:33180771 fatcat:43xebbok6repzjevew4eajxqmm

Omics Potential in Herbicide-Resistant Weed Management

Eric L. Patterson, Christopher Saski, Anita Küpper, Roland Beffa, Todd A. Gaines
2019 Plants  
Basic plant biology and genomics have incorporated these technologies, while some challenges remain for use in applied biology.  ...  Weed science, on the whole, is still learning how to integrate omics technologies into the discipline; however, omics techniques are more frequently being implemented in new and creative ways to address  ...  Furthermore, NSF-funded labs have produced easy to use online tools like the Genome Sequence Annotation Server (GenSAS) that provides a pipeline for de novo gene prediction and whole genome structural  ... 
doi:10.3390/plants8120607 pmid:31847327 pmcid:PMC6963460 fatcat:nj7jftut2fatrmf57nouppyliy

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

Ana Elena Pérez-Cobas, Laura Gomez-Valero, Carmen Buchrieser
2020 Microbial Genomics  
Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content.  ...  Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified.  ...  For eukaryotes, there are also specific tools for functional annotation, such as the previously mentioned MAKER2, or the Genome Sequence Annotation Server (GenSAS) [134] , which has recently become available  ... 
doi:10.1099/mgen.0.000409 pmid:32706331 fatcat:lv23zgejzzf45pmetzsb52kdlm

Genomics and bioinformatics resources for translational science in Rosaceae

Sook Jung, Dorrie Main
2013 Plant Biotechnology Reports  
These include annotated whole genome sequences, transcriptome and expression data, proteomic and metabolomic data, genotypic and phenotypic data, and genetic and physical maps.  ...  Analysis, storage, integration and dissemination of these data using bioinformatics tools and databases are essential to provide utility of the data for basic, translational and applied research.  ...  The Genome Sequence Annotation Server (GenSAS) (Lee et al. 2011) , an online annotation tool that provides a customizable automated pipeline for whole genome structural annotation, will be available for  ... 
doi:10.1007/s11816-013-0282-3 pmid:24634697 pmcid:PMC3951882 fatcat:4jygw6x3enas7bhe4yic7m76ou

The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants

Joshua A. Udall, Evan Long, Thiruvarangan Ramaraj, Justin L. Conover, Daojun Yuan, Corrinne E. Grover, Lei Gong, Mark A. Arick, Rick E. Masonbrink, Daniel G. Peterson, Jonathan F. Wendel
2019 Frontiers in Plant Science  
A series of structural rearrangements were identified comparing the de novo G. kirkii genome sequence to genome sequences of Gossypium, including chromosome fusions and inversions.  ...  We generated a high-quality genome sequence of Gossypioides kirkii (n = 12) using PacBio, Bionano, and Hi-C technologies, and compared this assembly to genome sequences of Kokia (n = 12) and Gossypium  ...  Gene annotations were created using GenSAS 5.0 (Lee et al., 2011) , an online integrated genome sequence annotation pipeline. BUSCO analysis was conducted to test for annotation completeness.  ... 
doi:10.3389/fpls.2019.01541 pmid:31827481 pmcid:PMC6890844 fatcat:yesw4poazzdrpf5clgoja73xzi

A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae

Kevin Weitemier, Shannon C.K. Straub, Mark Fishbein, C. Donovan Bailey, Richard C. Cronn, Aaron Liston
2019 PeerJ  
The genome was sequenced to 80.4× depth and the draft assembly contains 54,266 scaffolds ≥1 kbp, with N50 = 3,415 bp, representing 37% (156.6 Mbp) of the estimated 420 Mbp genome.  ...  A total of 14,474 protein-coding genes were identified based on transcript evidence, closely related proteins, and ab initio models, and 95% of genes were annotated.  ...  The Oregon State University Center for Genome Research and Biocomputing for expert sequencing facilities and computational infrastructure.  ... 
doi:10.7717/peerj.7649 pmid:31579586 pmcid:PMC6756140 fatcat:6m2eskfoijemvjffzoaqmv4qsy

A Web-Based Tool for Automatic Detection and Visualization of DNA Differentially Methylated Regions

Lisardo Fernández, Ricardo Olanda, Mariano Pérez, Juan M. Orduña
2021 Electronics  
The performance evaluation results show that this web-based version of HPG-DHunter tool improves the response time offered to the user, also offering an improved interface and higher visualization quality  ...  online platform that provide a pipeline for whole genome structural and functional annotation for eukaryotes and prokaryotes.  ...  [41] , designed for genome annotation of influenza virus, or MAKER Web Annotation Service [42] , a web-accessible graphical user interface for the MAKER annotation pipeline.  ... 
doi:10.3390/electronics10091083 fatcat:pppib5grtjg2vpdsoh47ggpxia

Chromosome-specific polymorphic SSR markers in tropical eucalypt species using low coverage whole genome sequences: systematic characterization and validation

Maheswari Patturaj, Aiswarya Munusamy, Nithishkumar Kannan, Ulaganathan Kandasamy, Yasodha Ramasamy
2021
The genomic resources generated in this study would provide an impetus to integrate genomics in marker-trait associations and breeding of tropical eucalypts.  ...  Low coverage (10×) genome sequencing was used to find polymorphic SSRs between the individuals.  ...  An online integrated genome sequence annotation pipeline Gen-SAS v6.0 [24] was used to annotate the pseudomolecules of four Eucalyptus individuals.  ... 
doi:10.5808/gi.21031 pmid:34638180 pmcid:PMC8510864 fatcat:5w5v3x7wsfhtjpumxb76e5gfbm

The somatic evolution of the canine transmissible venereal tumour

Adrian Baez Ortega, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository, Elizabeth Murchison
2020
This cancer first arose in an individual dog several thousand years ago, and has since survived by transfer of living cancer cells to new hosts during coitus.  ...  The second chapter describes the identification, annotation and preliminary analysis of the genetic variation found in CTVT tumours and their host dogs.  ...  Genomic annotation summary presenting the lengths (in megabases, Mb) of genomic regions for different annotation categories, across the entire CanFam3.1 reference genome and in the genomic regions sequenced  ... 
doi:10.17863/cam.52103 fatcat:n2jtlbquhjaeraqzyt56too6dq