DNA2App: Mobile sequence analyser

Sim, Jia-Zhi; Nguyen, Phi-Vu; Zang, Yu; Gan, Samuel Ken‐En

doi:10.1186/s41070-016-0004-7

Cited by 6 publications

(3 citation statements)

References 6 publications

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“…Sequence assembly and alignment of HIV-1 sequences were performed using the YAQAAT Webserver [ 78 ]. DNA2App [ 79 ] was used to analyze nucleotide and amino acid sequences. Mutations in the cDNA gene sequences were identified by multiple sequence alignments with characterized HIV-1 sequences from the Los Alamos sequence database [ 80 ].…”

Section: Methodsmentioning

confidence: 99%

Spontaneous Mutations in HIV-1 Gag, Protease, RT p66 in the First Replication Cycle and How They Appear: Insights from an In Vitro Assay on Mutation Rates and Types

Yeo

Koh

Yap

et al. 2020

IJMS

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While drug resistant mutations in HIV-1 are largely credited to its error prone HIV-1 RT, the time point in the infection cycle that these mutations can arise and if they appear spontaneously without selection pressures both remained enigmatic. Many HIV-1 RT mutational in vitro studies utilized reporter genes (LacZ) as a template to investigate these questions, thereby not accounting for the possible contribution of viral codon usage. To address this gap, we investigated HIV-1 RT mutation rates and biases on its own Gag, protease, and RT p66 genes in an in vitro selection pressure free system. We found rare clinical mutations with a general avoidance of crucial functional sites in the background mutations rates for Gag, protease, and RT p66 at 4.71 × 10−5, 6.03 × 10−5, and 7.09 × 10−5 mutations/bp, respectively. Gag and p66 genes showed a large number of ‘A to G’ mutations. Comparisons with silently mutated p66 sequences showed an increase in mutation rates (1.88 × 10−4 mutations/bp) and that ‘A to G’ mutations occurred in regions reminiscent of ADAR neighbor sequence preferences. Mutational free energies of the ‘A to G’ mutations revealed an avoidance of destabilizing effects, with the natural p66 gene codon usage providing barriers to disruptive amino acid changes. Our study demonstrates the importance of studying mutation emergence in HIV genes in a RT-PCR in vitro selection pressure free system to understand how fast drug resistance can emerge, providing transferable applications to how new viral diseases and drug resistances can emerge.

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Section: Methodsmentioning

confidence: 99%

Spontaneous Mutations in HIV-1 Gag, Protease, RT p66 in the First Replication Cycle and How They Appear: Insights from an In Vitro Assay on Mutation Rates and Types

Yeo

Koh

Yap

et al. 2020

IJMS

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“…Smartphones and tablet are increasingly popular for doing scientific analysis in recent years . Analysis of nucleic sequences is a common task in many fields of biological research, from genetic data analysis to understanding of human disease causations.…”

Section: Introductionmentioning

confidence: 99%

OligoCOOL: A mobile application for nucleotide sequence analysis

Khorsand

Khammari

Shirvanizadeh

et al. 2019

Biochem Molecular Bio Educ

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Today smartphones are inseparable parts of modern life and are capable of performing many desktop computers' tasks such as scientific analysis with greater convenience. Here, we present OligoCOOL, which is an Android application for analyzing nucleic sequences. This application enables users to perform several common biomedical analyses for a given nucleotide sequence. OligoCOOL is a freely accessible Android app at http://bioinf.modares.ac.ir/software/OligoCOOL, which can be a suitable tool for the experimental design in the laboratories. This application also can be used to learn the basics of nucleotide sequence analysis.

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“…To benefit such processes, apps (e.g. DNA2app, see Sim et al, 2016) allow users to analyse a sequence of interest, showing all possible restriction sites. (Table 7) Apps in this category are the most common.…”

Section: Peripheral Device Dependants (Table 4)mentioning

confidence: 99%

The world of biomedical apps: their uses, limitations, and potential

Gan

Poon

2016

Sci Phone Appl Mob Devices

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Many significant biomedical discoveries of old were made in the private property of famous scientists e.g. Leeuwenhoek and Archimedes. Today, discoveries are made in brightly-lit, hi-tech, ergonomic buildings that house research institutes. While such development is advantageous in many aspects, the spatial restriction of research into well-organized structures may delay and limit the spontaneity necessary for discoveries. The smartphone and peripheral mobile devices have the potential to not only increase the productivity and mobility of biomedical research, but also restore some freedom from spatial constraints. One possible way this can occur is the development of a mobile biomedical lab that allows researchers to carry out core research processes 'on-the-go' without being spatially restrained within a building or availability of equipment. For this exciting prospect, we surveyed the Google and Apple app stores, discussing the limitations and the potential of this area. Based on the developments, it appears to be just a matter of time before the majority of biomedical labs processes and equipment become mobile, centred on the smartphone and peripheral devices.

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DNA2App: Mobile sequence analyser

Cited by 6 publications

References 6 publications

Spontaneous Mutations in HIV-1 Gag, Protease, RT p66 in the First Replication Cycle and How They Appear: Insights from an In Vitro Assay on Mutation Rates and Types

Spontaneous Mutations in HIV-1 Gag, Protease, RT p66 in the First Replication Cycle and How They Appear: Insights from an In Vitro Assay on Mutation Rates and Types

OligoCOOL: A mobile application for nucleotide sequence analysis

The world of biomedical apps: their uses, limitations, and potential

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