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
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
An assessment of genome annotation coverage across the bacterial tree of life
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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
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
Lost and Found: Re-searching and Re-scoring Proteomics Data Aids Genome Annotation and Improves Proteome Coverage
Sign Up to like & getrecommendations! Published in 2020 at "mSystems"
DOI: 10.1128/msystems.00833-20
Abstract: Delineation of open reading frames (ORFs) causes persistent inconsistencies in prokaryote genome annotation. We demonstrate that by advanced (re)analysis of omics data, a higher proteome coverage and sensitive detection of unannotated ORFs can be achieved,… read more here.
Keywords: lost found; found searching; proteome coverage; genome annotation ... See more keywords
VARUS: sampling complementary RNA reads from the sequence read archive
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DOI: 10.1186/s12859-019-3182-x
Abstract: BackgroundVast amounts of next generation sequencing RNA data has been deposited in archives, accompanying very diverse original studies. The data is readily available also for other purposes such as genome annotation or transcriptome assembly. However,… read more here.
Keywords: read archive; annotation; varus; genome annotation ... See more keywords
EMBLmyGFF3: a converter facilitating genome annotation submission to European Nucleotide Archive
Sign Up to like & getrecommendations! Published in 2018 at "BMC Research Notes"
DOI: 10.1186/s13104-018-3686-x
Abstract: ObjectiveThe state-of-the-art genome annotation tools output GFF3 format files, while this format is not accepted as submission format by the International Nucleotide Sequence Database Collaboration (INSDC) databases. Converting the GFF3 format to a format accepted… read more here.
Keywords: format; submission; annotation; gff3 format ... See more keywords
StateHub-StatePaintR: rapid and reproducible chromatin state evaluation for custom genome annotation
Sign Up to like & getrecommendations! Published in 2018 at "F1000Research"
DOI: 10.12688/f1000research.13535.1
Abstract: Genome annotation is critical to understand the function of disease variants, especially for clinical applications. To meet this need there are segmentations available from public consortia reflecting varying unsupervised approaches to functional annotation based on… read more here.
Keywords: state; chromatin state; annotation; statehub ... See more keywords