Structural and Functional Annotation of Eukaryotic Genomes with GenSAS

Humann, Jodi L.; Lee, Taein; Ficklin, Stephen P.; Main, Dorrie

doi:10.1007/978-1-4939-9173-0_3

Cited by 96 publications

(74 citation statements)

References 35 publications

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“…Among these, we have the popular Prokka annotation tool [131], DFAST [132], which is especially useful to transfer annotations from other genomes, or the National Center for Biotechnology Information (NCBI) tool, PGAP [133]. 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. However, none of the previously mentioned tools has been developed specifically to cope with the typical problems associated with MAGs, such as poor quality assembly, possible contamination with foreign genes, or lack of close reference genomes.…”

Section: Wgs Metagenomicsmentioning

confidence: 99%

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

2020

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Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. 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. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.

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Section: Wgs Metagenomicsmentioning

confidence: 99%

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

2020

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“…Due to the high demand from researchers working on model systems, NGS data analysis can be performed through several publicly available platforms, for example the NSF-funded CyVerse with data storage and bioinformatic tools through the Discovery Environment web interface [51], or the Galaxy project [52]. 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 and functional annotation [53]. More tools that are weed science specific may need to be developed or adapted from other existing tools; for instance, a database of consistent annotations and gene ontologies.…”

Section: Methods Standardization For Utilizing Ngs In Weed Sciencementioning

confidence: 99%

Omics Potential in Herbicide-Resistant Weed Management

Patterson

Saski

Küpper

et al. 2019

Plants

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The rapid development of omics technologies has drastically altered the way biologists conduct research. 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 basic questions in weed biology as well as the more practical questions of improving weed management. This has been especially true in the subdiscipline of herbicide resistance where important questions are the evolution and genetic basis of herbicide resistance. This review examines the advantages, challenges, potential solutions, and outlook for omics technologies in the discipline of weed science, with examples of how omics technologies will impact herbicide resistance studies and ultimately improve management of herbicide-resistant populations.

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“…The polished assembly was annotated using Prodigal v2.6.3 [61]. The annotation gff3 le was loaded into in the GenSAS suite version 6.0 [62], after which functional analyses was conducted in the suite using InterProScan version 5.25-68.0 [63] and the ab initio predicted proteins were identi ed using blastp [64] by conducting a protein vs protein search against the SwissProt protein data set to determine best matches. Protein sequences were analyzed for signal peptides using the SignalP v5.0 [65].…”

Section: Genome Annotationmentioning

confidence: 99%

Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides

Saud

Hitchings

Butt

2020

Preprint

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DNA viruses can exploit host cellular epigenetic processes to their advantage; however, the epigenome status of most DNA viruses remains undetermined. Third generation sequencing technologies allow for the identification of modified nucleotides from sequencing experiments without specialized sample preparation, permitting the detection of non-canonical epigenetic modifications that may distinguish viral nucleic acid from that of their host, thus identifying attractive targets for advanced therapeutics and diagnostics. We present a novel nanopore de novo assembly pipeline used to assemble a misidentified Camelpox vaccine. Two confirmed deletions of this vaccine strain in comparison to the closely related Vaccinia virus strain modified vaccinia Ankara make it one of the smallest non-vector derived orthopoxvirus genomes to be reported. Annotation of the assembly revealed a previously unreported signal peptide at the start of protein A38 and several signal peptides that were found to differ from those previously described. Putative epigenetic modifications around various motifs have been identified and the assembly confirmed previous work showing the vaccine genome to most closely resemble that of Vaccinia virus strain Modified Vaccinia Ankara. The pipeline may be used for other DNA viruses, increasing the understanding of DNA virus evolution, virulence, host preference, and epigenomics.

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Structural and Functional Annotation of Eukaryotic Genomes with GenSAS

Cited by 96 publications

References 35 publications

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

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

Omics Potential in Herbicide-Resistant Weed Management

Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides

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