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Three minimal sequences found in Ebola virus genomes and absent from human DNA: Fig. 1
2015
Bioinformatics
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Only three absent sequences of length 12 exist and they consistently appear at the same location on two of the Ebola virus proteins, in all Ebola virus genomes, but nowhere in the human genome. ...
Results: Analysis of Ebola virus genomes from the current outbreak reveals the presence of short DNA sequences that appear nowhere in the human genome. ...
Fig. 1 . 1 Ebola virus minimal absent words relatively to the human complete genome. ...
doi:10.1093/bioinformatics/btv189
pmid:25840045
pmcid:PMC4514932
fatcat:67o37jz6hrhqfpy36fdmoti3ra
Persistent minimal sequences of SARS-CoV-2
2020
Bioinformatics
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Results Analysis of SARS-CoV-2 genomes from the current outbreak reveals the presence of short persistent DNA/RNA sequences that are absent from the human genome and transcriptome (PmRAWs). ...
to the virus and host genome distributions. ...
Discussion In this article, we revealed the existence of short DNA/RNA sequences, with sizes comprehended between 12 and 17, that are present in 93 SARS-CoV-2 genomes and absent from the human genome and ...
doi:10.1093/bioinformatics/btaa686
pmid:32730589
fatcat:gteumzni4reyzgjgumv7mxblwy
Absent words and the (dis)similarity analysis of DNA sequences: an experimental study
2016
BMC Research Notes
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An absent word with respect to a sequence is a word that does not occur in the sequence as a factor; an absent word is minimal if all its factors on the other hand occur in that sequence. ...
The motivation and rationale of our work comes from the potential advantage of being able to extract as little information as possible from large genomic sequences to reach the goal of comparing sequences ...
Sohel Rahman was on a Sabbatical Leave from BUET and was visiting King's College, London. ...
doi:10.1186/s13104-016-1972-z
pmid:27004958
pmcid:PMC4804535
fatcat:hnpd33l5b5gbxlar6mvrlrcxvq
Significant non-existence of sequences in genomes and proteomes
2021
Nucleic Acids Research
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Minimal absent words (MAWs) are minimal-length oligomers absent from a genome or proteome. ...
Significant human MAWs are frequently present in prokaryotes, suggesting immune function, but rarely present in human viruses, indicating viral mimicry of the host. ...
ACKNOWLEDGEMENTS We thank and acknowledge helpful conversations with Sara Zanivan (CRUK Beatson Institute), Spyros Lytras (MRC -University of Glasgow Centre for Virus Research), Kiyoshi ...
doi:10.1093/nar/gkab139
pmid:33693858
fatcat:36xnboxrejbifgouvty4addqt4
G-Quadruplexes: More Than Just a Kink in Microbial Genomes
2018
Trends in Microbiology
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G-quadruplexes (G4s) are noncanonical nucleic acid secondary structures formed by guanine-rich DNA and RNA sequences. ...
Importantly, G4s in hepatitis B virus (HBV) and hepatitis C virus (HCV) genomes modulate genes crucial for virus replication. ...
Human papilloma virus (HPV) is a DNA virus that causes warts and cervical cancer. ...
doi:10.1016/j.tim.2018.08.011
pmid:30224157
pmcid:PMC7127049
fatcat:idh4z5ii5nhifjatepp4llvl3y
A flexible format LAMP assay for rapid detection of Ebola virus
2020
PLoS Neglected Tropical Diseases
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The assays are rapid, (as fast as 5-7.25 mins for real-time formats) and robust, detecting Ebola virus RNA in presence of minimally diluted bodily fluids. ...
Ebola virus is highly infectious and prompt diagnosis and triage is crucial in preventing further spread within community and healthcare settings. ...
We would also like to acknowledge Dr Patrick Deegan from the Defence Science and Technology Laboratory (DSTL) for his assistance with the Probit analysis. ...
doi:10.1371/journal.pntd.0008496
pmid:32735587
fatcat:rdqrygrmkbhd5aseb327brjvei
Ebola Virus Defective Interfering Particles and Persistent Infection
1999
Virology
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Minimal promoters for Ebola virus replication were found to be contained within 156 and 177 nucleotide regions of the genomic and antigenomic RNA 3Ј termini, respectively, based on the length of authentic ...
It was found that serial undiluted virus passages quickly resulted in production of an evolving population of virus minireplicons possessing both deletion and copyback type DI genome rearrangements. ...
ACKNOWLEDGMENTS We are grateful to Tony Sanchez for communicating sequence data that was unpublished at the time of initiation of this project and for providing some of the plasmids used for production ...
doi:10.1006/viro.1999.9915
pmid:10489346
fatcat:g66s25usvzcijp5nkjgddqmjfa
Significant non-existence of sequences in genomes and proteomes
[article]
2020
bioRxiv
pre-print
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Nullomers are minimal-length oligomers absent from a genome or proteome. ...
We survey genomes and proteomes covering the diversity of life, and find thousands of significant absent sequences. ...
Acknowledgements We thank and acknowledge helpful conversations with Sara Zanivan ( ...
doi:10.1101/2020.06.25.170431
fatcat:wfesuiyarjbczino7rulnrante
New and Re-emerging Viral Pathogens
1999
Journal of King Abdulaziz University-Medical Sciences
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Of these are HIV, Hantavirus, monkeypox virus, dengue virus, influenza virus 1&5 NI, Kaposi's sarcomaassociated herpes virus (KSHV), Boma disease virus, Ebola virus, other haemorrhagic fever viruses, Al-Khorrna ...
virus, hepatitis G virus, Calicivirus gastroenteritis, Enteroviral meningitis, Bovine prions and nvCJD. ...
This technique relies on the use of highly conserved DNA sequences, such as ribosomal'RNA gene sequences from known organisms, to amplify DNA from related organisms not yet discovered. ...
doi:10.4197/med.7-1.3
fatcat:muqeuxx66nhrvl53dxb2eub23i
Antiviral Therapy
[chapter]
2016
Viral Pathogenesis
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NHP: 100% survival for
Marburg virus (using
Marburg sequence)
and 50-60% survival
for Ebola using Ebola
sequence.
Phase I safety study
completed.
Tolerability
demonstrated. ...
Inhibits Ebola
virus replication by binding
to RNA in sequence-specific
manner to VP24 gene. Specific
to this strain of Ebola. ...
doi:10.1016/b978-0-12-800964-2.00020-3
fatcat:n24ypr3gerfn7dz5gfeik5zb7i
Hunting Viral Receptors Using Haploid Cells
2015
Annual Review of Virology
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In this review we discuss the most commonly employed methods for virus receptor discovery, specifically highlighting the use of forward genetic screens in human haploid cells. ...
As an example, haploid genetic screens identified the lysosomal proteins, NPC1 and LAMP1, as intracellular receptors for Ebola virus and Lassa virus, respectively. ...
We thank David Schneider, Peter Sarnow, Pascale Guiton and Karim Majzoub for carefully reading this review and Christopher Wood for his help in preparation of the figures. ...
doi:10.1146/annurev-virology-100114-055119
pmid:26958914
pmcid:PMC4982367
fatcat:3xaij67mvrcorhug44khrsntvu
emMAW: computing minimal absent words in external memory
2017
Bioinformatics
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For instance, three minimal absent words of the human genome were found in Ebola virus genomes (Silva et al., Bioinf., 2015). ...
Motivation: The biological significance of minimal absent words has been investigated in genomes of organisms from all domains of life. ...
We computed all minimal absent words of length at most 11 for each sequence. We considered both DNA strands. ...
doi:10.1093/bioinformatics/btx209
pmid:28407038
fatcat:dmmhjtayejgbxhd2ceunymlmh4
Ebola Virus Encodes Two microRNAs in Huh7-Infected Cells
2022
International Journal of Molecular Sciences
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Here, we characterized the miRNA transcriptome of cultured human liver cells infected or not with either of the two Ebola virus (EBOV) variants: Mayinga or Makona; or with Reston virus (RESTV). ...
From the miRDB database, miR-MAY-251 and miR-MAK-403 displayed on average more than 700 potential human host target candidates, 25% of which had a confidence score higher than 80%. ...
The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results. ...
doi:10.3390/ijms23095228
pmid:35563619
pmcid:PMC9106010
fatcat:ms4chy7msrhfvh225zypua6ave
Assessment of Epstein-Barr virus nucleic acids in gastric but not in breast cancer by next-generation sequencing of pooled Mexican samples
2016
Memórias do Instituto Oswaldo Cruz
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While we did not find viral sequences in tissues from BrC patients, multiple reads matching Epstein-Barr virus (EBV) sequences were found in GC tissues. ...
Wide genome sequencing (WGS) technologies allow searching for viral agents in tissues of patients with cancer. ...
Several viral hits from human papillomavirus (HPV) 16, mouse mammary tumour virus (MMTV), and Epstein-Barr virus (EBV) were mapped from human-viral inputs mimicking genomic load present in tumours associated ...
doi:10.1590/0074-02760150405
pmid:26910355
pmcid:PMC4804503
fatcat:sqrm7wgdjncg7fg7uonx4ghewa
Genome sequence and comparative virulence of raccoonpox virus: the first North American poxvirus sequence
2015
Journal of General Virology
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RCNV contained one unique genome region containing approximately 1 kb of DNA sequence that is not present in any reported poxvirus. ...
We report here the complete genome sequence of raccoonpox virus (RCNV), a naturally occurring North American poxvirus. ...
., East Carolina University, and a Natural Sciences and Engineering Research Council Discovery Grant to C. U. ...
doi:10.1099/vir.0.000202
pmid:26023150
fatcat:5izisnbtcfhi7poxiohevwh3yu
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