Phage Genome Annotation Using the RAST Pipeline.
Sign Up to like & getrecommendations! Published in 2018 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7343-9_17
Abstract: Phages are complex biomolecular machineries that have to survive in a bacterial world. Phage genomes show many adaptations to their lifestyle such as shorter genes, reduced capacity for redundant DNA sequences, and the inclusion of… read more here.
Keywords: pipeline; phage genome; phage; annotation ... See more keywords
Multi-Genome Annotation with AUGUSTUS.
Sign Up to like & getrecommendations! Published in 2019 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-9173-0_8
Abstract: Comparing multiple related genomes can help to improve their structural annotation. The accuracy and consistency of the predicted exon-intron structures of the protein coding genes can be higher when considering all genomes at once rather… read more here.
Keywords: augustus; multi genome; annotation; annotation augustus ... See more keywords
Chromosome-level genome and annotation of the tetraploid Rhodiola kirilowii
Sign Up to like & getrecommendations! Published in 2025 at "Scientific Data"
DOI: 10.1038/s41597-025-04962-5
Abstract: Rhodiola kirilowii, a perennial medical herb native to China, is highly valued for its detoxification and anti-swelling properties, as well as its role as an adaptogen, making it an intriguing subject for understanding its medicinal… read more here.
Keywords: level genome; rhodiola kirilowii; genome annotation; chromosome level ... See more keywords
Fast Context-Aware Analysis of Genome Annotation Colocalization
Sign Up to like & getrecommendations! Published in 2024 at "Journal of Computational Biology"
DOI: 10.1089/cmb.2024.0667
Abstract: An annotation is a set of genomic intervals sharing a particular function or property. Examples include genes or their exons, sequence repeats, regions with a particular epigenetic state, and copy number variants. A common task… read more here.
Keywords: aware analysis; context aware; genome annotation; annotation ... See more keywords
Genome annotation of disease-causing microorganisms
Sign Up to like & getrecommendations! Published in 2021 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbab004
Abstract: Humans have coexisted with pathogenic microorganisms throughout its history of evolution. We have never halted the exploration of pathogenic microorganisms. With the improvement of genome-sequencing technology and the continuous reduction of sequencing costs, an increasing… read more here.
Keywords: disease causing; causing microorganisms; annotation disease; annotation ... See more keywords
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation
Sign Up to like & getrecommendations! Published in 2021 at "Nucleic acids research"
DOI: 10.1093/nar/gkaa1105
Abstract: The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains nearly 200 000 bacterial and archaeal genomes and 150 million proteins with up-to-date annotation. Changes in the Prokaryotic Genome Annotation Pipeline… read more here.
Keywords: refseq; protein family; annotation; prokaryotic genome ... See more keywords
Bakta Web – rapid and standardized genome annotation on scalable infrastructures
Sign Up to like & getrecommendations! Published in 2025 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkaf335
Abstract: Abstract The Bakta command line application is widely used and one of the most established tools for bacterial genome annotation. It balances comprehensive annotation with computational efficiency via alignment-free sequence identifications. However, the usage of… read more here.
Keywords: command line; genome annotation; bakta web; web rapid ... See more keywords
An assessment of genome annotation coverage across the bacterial tree of life
Sign Up to like & getrecommendations! Published in 2020 at "Microbial Genomics"
DOI: 10.1099/mgen.0.000341
Abstract: Although gene-finding in bacterial genomes is relatively straightforward, the automated assignment of gene function is still challenging, resulting in a vast quantity of hypothetical sequences of unknown function. But how prevalent are hypothetical sequences across… read more here.
Keywords: completeness; annotation coverage; annotation; annotation completeness ... See more keywords
Comparative Annotation Toolkit (CAT) - Simultaneous Clade and Personal Genome Annotation
Sign Up to like & getrecommendations! Published in 2018 at "Genome research"
DOI: 10.1101/gr.233460.117
Abstract: The recent introductions of low-cost, long-read, and read-cloud sequencing technologies coupled with intense efforts to develop efficient algorithms have made affordable, high-quality de novo sequence assembly a realistic proposition. The result is an explosion of… read more here.
Keywords: comparative annotation; annotation; annotation toolkit; genome annotation ... See more keywords
Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
Sign Up to like & getrecommendations! Published in 2024 at "Genome Research"
DOI: 10.1101/gr.279864.124
Abstract: While the production of a draft genome has become more accessible due to long-read sequencing, the annotation of these new genomes has not been developed at the same pace. Long-read RNA sequencing offers a promising… read more here.
Keywords: read rna; long read; genome annotation; annotation ... See more keywords
Long-Read Annotation: Automated Eukaryotic Genome Annotation Based on Long-Read cDNA Sequencing1[OPEN]
Sign Up to like & getrecommendations! Published in 2018 at "Plant Physiology"
DOI: 10.1104/pp.18.00848
Abstract: The long Read Annotation (LoReAn) pipeline provides automated genome annotation with superior performance by incorporating single-molecule cDNA sequencing data. Single-molecule full-length complementary DNA (cDNA) sequencing can aid genome annotation by revealing transcript structure and alternative… read more here.
Keywords: long read; annotation; read annotation; cdna ... See more keywords