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Three minimal sequences found in Ebola virus genomes and absent from human DNA: Fig. 1

Raquel M. Silva, Diogo Pratas, Luísa Castro, Armando J. Pinho, Paulo J. S. G. Ferreira
2015 Bioinformatics  
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

Diogo Pratas, Jorge M Silva, Pier Luigi Martelli
2020 Bioinformatics  
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

Mohammad Saifur Rahman, Ali Alatabbi, Tanver Athar, Maxime Crochemore, M. Sohel Rahman
2016 BMC Research Notes  
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

Grigorios Koulouras, Martin C Frith
2021 Nucleic Acids Research  
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

Nandhini Saranathan, Perumal Vivekanandan
2018 Trends in Microbiology  
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

Laura C. Bonney, Robert J. Watson, Gillian S. Slack, Andrew Bosworth, Nadina I. Vasileva Wand, Roger Hewson, Alyssa E. Barry
2020 PLoS Neglected Tropical Diseases  
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

Philippe Calain, Martha C. Monroe, Stuart T. Nichol
1999 Virology  
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]

Grigorios Koulouras, Martin C. Frith
2020 bioRxiv   pre-print
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  
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]

Douglas D. Richman, Neal Nathanson
2016 Viral Pathogenesis  
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

Sirika Pillay, Jan E. Carette
2015 Annual Review of Virology  
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

Alice Héliou, Solon P Pissis, Simon J Puglisi, Inanc Birol
2017 Bioinformatics  
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

Idrissa Diallo, Zeinab Husseini, Sara Guellal, Elodie Vion, Jeffrey Ho, Robert A. Kozak, Gary P. Kobinger, Patrick Provost
2022 International Journal of Molecular Sciences  
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

Ezequiel M Fuentes-Pananá, Violeta Larios-Serrato, Alfonso Méndez-Tenorio, Abigail Morales-Sánchez, Carlos F Arias, Javier Torres
2016 Memórias do Instituto Oswaldo Cruz  
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

Clare Fleischauer, Rachel L. Roper, Gwendolyn J. B. Jones, Joseph Victoria, Chris Upton
2015 Journal of General Virology  
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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