DNAApp: a mobile application for sequencing data analysis

Nguyen, Phi-Vu; Verma, Chandra; Gan, Samuel Ken‐En

doi:10.1093/bioinformatics/btu525

Cited by 23 publications

(16 citation statements)

References 4 publications

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“…All plasmids for transfection were extracted using Quintech plasmid miniprep kit 27 (Cat no: QT100–1101, Quintech Lifesciences Pte Ltd). All cloning steps were sequence validated using DNAapp 28 and analyzed using MAFFT, 29 ANNIE, 17 and SignalP 4.0 18 …”

Section: Methodsmentioning

confidence: 99%

Discovery of a novel splice variant of Fcar (CD89) unravels sequence segments necessary for efficient secretion: A story of bad signal peptides and good ones that nevertheless do not make it

Lua

Ling

et al. 2017

Cell Cycle

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The IgA receptor, Fcar (CD89) consists of 5 sequence segments: 2 segments (S1, S2) forming the potential signal peptide, 2 extracellular EC domains that include the IgA binding site, and the transmembrane and cytoplasmic tail (TM/C) region. Numerous Fcar splice variants have been reported with various combinations of the sequence segments mentioned above. Here, we report a novel splice variant termed variant APD isolated from a healthy volunteer that lacks only the IgA-binding EC1 domain. Despite possessing the complete signal peptide S1+S2, the variant APD is only found in the intracellular space whereas the wild-type variant 1 is efficiently secreted and variant 4 leaks to the extracellular space. Further mutational experiments involving signal peptide replacements, cleavage site modifications, and studies on alternative isoforms demonstrate that despite the completeness of the signal peptide motif, the presence of the EC1 domain is essential for efficient extracellular export.

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Section: Methodsmentioning

confidence: 99%

Discovery of a novel splice variant of Fcar (CD89) unravels sequence segments necessary for efficient secretion: A story of bad signal peptides and good ones that nevertheless do not make it

Lua

Ling

et al. 2017

Cell Cycle

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“…Some aid in opening sequencing files (e.g. DNAapp, see Nguyen, et al, 2014), bringing mobility to an analysis that was once limited to desktop/laptops. With these apps, pictures of sequences can also be processed (e.g.…”

Section: Reviewmentioning

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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“…This demand is highlighted in the numerous new biomedical apps that increase the portability and efficiency of biological research. Examples of apps that do this include DNAApp (Nguyen et al 2014), GelApp (Sim et al 2015), and YASARA View (Krieger & Vriend 2014). These aid in everyday experiments (see lab examples (Poh & Gan 2014a;Poh & Gan 2014b)) to improve the presentation and accuracy of experimental data (see example (Ling et al 2015)).…”

Section: Introductionmentioning

confidence: 99%

“…When used together with "app enablers" like DNAApp (Nguyen et al 2014) which analyzes ab1 files, DNA2App can provide additional off-line analysis of sequencing data. While sharing certain similar features to our DNAApp, DNA2App was highly requested as it allows text input, and has added features (such as restriction enzymes, reverse translation) compared to only ab1 files analysis in DNAapp.…”

Section: Introductionmentioning

confidence: 99%

DNA2App: Mobile sequence analyser

Sim

Nguyen

Zang

et al. 2016

Sci Phone Appl Mob Devices

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Smartphones have changed the convenience of everyday life and promises to facilitate core biomedical research analysis. To materialize this for research, we created DNA2App, a free standalone native Android and iOS mobile application that analyzes nucleic acid and amino acid sequences. Boasting a built-in database of more than 240 restriction sites and the amino acid codon table, the app allows sequences to be reverse complemented, translated in all 3 frames and searched for restriction sites, and their GC content and melting point can be calculated. Supplemented by the features of exportation to FASTA format and copying to clipboard, results can be kept or easily stored and communicated. Combined, these features increase the ease and convenience of commonly used sequence analyses that every scientist can carry in their pockets.

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DNAApp: a mobile application for sequencing data analysis

Cited by 23 publications

References 4 publications

Discovery of a novel splice variant of Fcar (CD89) unravels sequence segments necessary for efficient secretion: A story of bad signal peptides and good ones that nevertheless do not make it

Discovery of a novel splice variant of Fcar (CD89) unravels sequence segments necessary for efficient secretion: A story of bad signal peptides and good ones that nevertheless do not make it

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

DNA2App: Mobile sequence analyser

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