scholarly journals Phage Genome Annotation Using the RAST Pipeline

2017 ◽  
pp. 231-238 ◽  
Author(s):  
Katelyn McNair ◽  
Ramy Karam Aziz ◽  
Gordon D. Pusch ◽  
Ross Overbeek ◽  
Bas E. Dutilh ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Phage Genome

scholarly journals A Method for Improving the Accuracy and Efficiency of Bacteriophage Genome Annotation

2019 ◽  
Vol 20 (14) ◽  
pp. 3391 ◽  
Author(s):  
Alicia Salisbury ◽  
Philippos K. Tsourkas
Keyword(s):  
Decision Making ◽  
Genome Annotation ◽  
Phage Genome ◽  
Labor Cost ◽  
Additional Benefit ◽  
Student Recruitment ◽  
Manual Curation ◽  
A Genome ◽  
Bacteriophage Genome ◽  
Genome Annotations

Bacteriophages are the most numerous entities on Earth. The number of sequenced phage genomes is approximately 8000 and increasing rapidly. Sequencing of a genome is followed by annotation, where genes, start codons, and functions are putatively identified. The mainstays of phage genome annotation are auto-annotation programs such as Glimmer and GeneMark. Due to the relatively small size of phage genomes, many groups choose to manually curate auto-annotation results to increase accuracy. An additional benefit of manual curation of auto-annotated phage genomes is that the process is amenable to be performed by students, and has been shown to improve student recruitment to the sciences. However, despite its greater accuracy and pedagogical value, manual curation suffers from high labor cost, lack of standardization and a degree of subjectivity in decision making, and susceptibility to mistakes. Here, we present a method developed in our lab that is designed to produce accurate annotations while reducing subjectivity and providing a degree of standardization in decision-making. We show that our method produces genome annotations more accurate than auto-annotation programs while retaining the pedagogical benefits of manual genome curation.

scholarly journals Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation

2020 ◽  
Vol 16 (11) ◽  
pp. e1008214
Author(s):  
Jolene Ramsey ◽  
Helena Rasche ◽  
Cory Maughmer ◽  
Anthony Criscione ◽  
Eleni Mijalis ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Phage Genome ◽  
Structural Annotation ◽  
Sequence Comparisons ◽  
User Training ◽  
Computationally Intensive ◽  
Modern Genomic ◽  
Training Need ◽  
User Friendly ◽  
Computational Analyses

In the modern genomic era, scientists without extensive bioinformatic training need to apply high-power computational analyses to critical tasks like phage genome annotation. At the Center for Phage Technology (CPT), we developed a suite of phage-oriented tools housed in open, user-friendly web-based interfaces. A Galaxy platform conducts computationally intensive analyses and Apollo, a collaborative genome annotation editor, visualizes the results of these analyses. The collection includes open source applications such as the BLAST+ suite, InterProScan, and several gene callers, as well as unique tools developed at the CPT that allow maximum user flexibility. We describe in detail programs for finding Shine-Dalgarno sequences, resources used for confident identification of lysis genes such as spanins, and methods used for identifying interrupted genes that contain frameshifts or introns. At the CPT, genome annotation is separated into two robust segments that are facilitated through the automated execution of many tools chained together in an operation called a workflow. First, the structural annotation workflow results in gene and other feature calls. This is followed by a functional annotation workflow that combines sequence comparisons and conserved domain searching, which is contextualized to allow integrated evidence assessment in functional prediction. Finally, we describe a workflow used for comparative genomics. Using this multi-purpose platform enables researchers to easily and accurately annotate an entire phage genome. The portal can be accessed at https://cpt.tamu.edu/galaxy-pub with accompanying user training material.

scholarly journals Phage Genome Annotation: Where to Begin and End

PHAGE ◽  
2021 ◽  
Vol 2 (4) ◽  
pp. 183-193
Author(s):  
Anastasiya Shen ◽  
Andrew Millard
Keyword(s):  
Genome Annotation ◽  
Phage Genome

scholarly journals Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Michael F. Z. Wang ◽  
Madhav Mantri ◽  
Shao-Pei Chou ◽  
Gaetano J. Scuderi ◽  
David W. McKellar ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Annotation ◽  
Gene Annotation ◽  
Active Regions ◽  
Sequencing Analysis ◽  
Biologically Relevant ◽  
Mole Rat ◽  
Genome Annotations ◽  
Cell Expression ◽  
High Quality Genome

AbstractConventional scRNA-seq expression analyses rely on the availability of a high quality genome annotation. Yet, as we show here with scRNA-seq experiments and analyses spanning human, mouse, chicken, mole rat, lemur and sea urchin, genome annotations are often incomplete, in particular for organisms that are not routinely studied. To overcome this hurdle, we created a scRNA-seq analysis routine that recovers biologically relevant transcriptional activity beyond the scope of the best available genome annotation by performing scRNA-seq analysis on any region in the genome for which transcriptional products are detected. Our tool generates a single-cell expression matrix for all transcriptionally active regions (TARs), performs single-cell TAR expression analysis to identify biologically significant TARs, and then annotates TARs using gene homology analysis. This procedure uses single-cell expression analyses as a filter to direct annotation efforts to biologically significant transcripts and thereby uncovers biology to which scRNA-seq would otherwise be in the dark.

Whole genome sequencing and genome annotation of Dermacoccus abyssi strain HZAU 226 isolated from spoiled eggs

Genomics ◽  
2020 ◽  
Author(s):  
Xinshuai Zhang ◽  
Yao Ruan ◽  
Wukang Liu ◽  
Qian Chen ◽  
Lihong Gu ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Annotation ◽  
Whole Genome

scholarly journals Phage genetic sites involved in lambda growth inhibition by the Escherichia coli rap mutant.

Genetics ◽  
1989 ◽  
Vol 121 (3) ◽  
pp. 401-409
Author(s):  
P Guzmán ◽  
G Guarneros
Keyword(s):  
Escherichia Coli ◽  
Growth Inhibition ◽  
Phage Genome ◽  
Bacteriophage Lambda ◽  
Phage Lambda ◽  
Wild Type ◽  
Attp Site

Abstract The rap mutation of Escherichia coli prevents the growth of bacteriophage lambda. We have isolated phage mutants that compensate for the host deficiency. The mutations, named bar, were genetically located to three different loci of the lambda genome: barI in the attP site, barII in the cIII ea10 region, and barIII within or very near the imm434 region. The level of lambda leftward transcription correlates with rap exclusion. Phage lambda mutants partially defective in the pL promoter or in pL-transcript antitermination showed a Bar- phenotype. Conversely, mutants constitutive for transcription from the pI or pL promoters were excluded more stringently by rap bacteria. We conclude that rap exclusion depends on the magnitude of transcription through the wild type bar loci in the phage genome.

Transcript map of the temperate Lactobacillus gasseri bacteriophage ϕadh

Microbiology ◽  
2003 ◽  
Vol 149 (10) ◽  
pp. 2987-2999 ◽  
Author(s):  
Eric Altermann ◽  
Bernhard Henrich
Keyword(s):  
Replication Origin ◽  
Phage Genome ◽  
Attachment Site ◽  
Genomic Region ◽  
Dna Packaging ◽  
Middle Region ◽  
Late Transcription ◽  
Early Transcription ◽  
Transcript Map ◽  
Overlapping Transcripts

Temporal transcription of phage ϕadh was analysed during lytic reproduction. Based on Northern hybridizations the phage genome was divided into regions of early, middle and late transcription. Eight groups of overlapping transcripts, probably originating from common precursors, were distinguished. Early transcription of a 10·9 kb region adjacent to the lytic/lysogenic switch started within the first 10 min of infection and produced three groups of mRNAs mostly related to DNA replication. Four middle transcripts were observed 30 min after infection, corresponding to an 8·5 kb genomic region, which started at the replication origin (ori) and encompassed a DNA packaging function and the cos site. Three groups of late transcripts were first observed 50 min after infection, corresponding to a 21·1 kb region between the middle region and the attachment site (attP), encoding functions for capsid morphogenesis and host cell lysis. A fourth group of late-appearing mRNAs was divergently transcribed from the 3·2 kb section between attP and the lytic/lysogenic switch, including the repressor and integrase genes. Except for one set of early mRNAs, all the transcripts persisted until the end of the reproduction cycle. Two confirmed and two predicted promoters were assigned to transcript 5′ ends in the early region.

scholarly journals Genome annotation by high-throughput 5' RNA end determination

2004 ◽  
Vol 101 (6) ◽  
pp. 1650-1655 ◽  
Author(s):  
B. J. Hwang ◽  
H.-M. Muller ◽  
P. W. Sternberg
Keyword(s):  
High Throughput ◽  
Genome Annotation
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