Computational Art Inspired on Genome Browsers

Leonardo ◽  
2019 ◽  
pp. 1-7
Author(s):  
Martin Calvino
Keyword(s):  
Arabidopsis Thaliana ◽  
Genome Sequence ◽  
Scientific Community ◽  
Sequence Data ◽  
Genome Browser ◽  
Genome Sequence Data ◽  
Genome Data ◽  
Bioinformatics Tools ◽  
Genome Browsers ◽  
Plant Arabidopsis Thaliana

This manuscript describes the genome browser of the plant Arabidopsis thaliana as inspirational object for creation of geometric artworks developed with code. Genome browsers are bioinformatics tools used by life scientists to access and visualize genome sequence data from species of interest. The artworks presented are inspired on genome sequence data and provide alternative aesthetic interpretations of genes and their genomic contexts derived from a subjective take of an individual artist on the conventional visualization of genome data accepted by the scientific community at large.

Drosophila genomes and the development of affordable molecular markers for species genotyping

Genome ◽  
2011 ◽  
Vol 54 (4) ◽  
pp. 341-347 ◽  
Author(s):  
Leigh Minuk ◽  
Alberto Civetta
Keyword(s):  
Molecular Markers ◽  
Genome Sequence ◽  
Sequence Data ◽  
Closely Related Species ◽  
Genome Sequence Data ◽  
Sequencing Errors ◽  
Genome Data ◽  
Indel Polymorphisms ◽  
Partial Genome ◽  
Rule Out

The recent completion of genome sequencing of 12 species of Drosophila has provided a powerful resource for hypothesis testing, as well as the development of technical tools. Here we take advantage of genome sequence data from two closely related species of Drosophila, Drosophila simulans and Drosophila sechellia, to quickly identify candidate molecular markers for genotyping based on expected insertion or deletion (indel) differences between species. Out of 64 candidate molecular markers selected along the second and third chromosome of Drosophila, 51 molecular markers were validated using PCR and gel electrophoresis. We found that the 20% error rate was due to sequencing errors in the genome data, although we cannot rule out possible indel polymorphisms. The approach has the advantage of being affordable and quick, as it only requires the use of bioinformatics tools for predictions and a PCR and agarose gel based assay for validation. Moreover, the approach could be easily extended to a wide variety of taxa with the only limitation being the availability of complete or partial genome sequence data.

scholarly journals The emergence of SARS-CoV-2 variants of concern is driven by acceleration of the evolutionary rate

2021 ◽  
Author(s):  
John H Tay ◽  
Ashleigh F Porter ◽  
Wytamma Wirth ◽  
Sebastian Duchene
Keyword(s):  
Molecular Evolution ◽  
Genome Sequence ◽  
Molecular Clock ◽  
Evolutionary Rate ◽  
Sequence Data ◽  
Rate Estimate ◽  
Genome Sequence Data ◽  
Genome Data ◽  
Phylogenetic Level ◽  
Clock Models

The ongoing SARS-CoV-2 pandemic has seen an unprecedented amount of rapidly generated genome data. These data have revealed the emergence of lineages with mutations associated to transmissibility and antigenicity, known as variants of concern (VOCs). A striking aspect of VOCs is that many of them involve an unusually large number of defining mutations. Current phylogenetic estimates of the evolutionary rate of SARS-CoV-2 suggest that its genome accrues around 2 mutations per month. However, VOCs can have around 15 defining mutations and it is hypothesised that they emerged over the course of a few months, implying that they must have evolved faster for a period of time. We analysed genome sequence data from the GISAID database to assess whether the emergence of VOCs can be attributed to changes in the evolutionary rate of the virus and whether this pattern can be detected at a phylogenetic level using genome data. We fit a range of molecular clock models and assessed their statistical fit. Our analyses indicate that the emergence of VOCs is driven by an episodic increase in the evolutionary rate of around 4-fold the background phylogenetic rate estimate that may have lasted several weeks or months. These results underscore the importance of monitoring the molecular evolution of the virus as a means of understanding the circumstances under which VOCs may emerge.

TIGER: inferring DNA replication timing from whole-genome sequence data

2021 ◽  
Author(s):  
Amnon Koren ◽  
Dashiell J Massey ◽  
Alexa N Bracci
Keyword(s):  
Dna Replication ◽  
Genome Sequence ◽  
Genomic Dna ◽  
Sequence Data ◽  
Replication Timing ◽  
Whole Genome Sequence ◽  
Supplementary Information ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Dna Replication Timing

Abstract Motivation Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges. Results We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale. Availability and Implementation TIGER is available at https://github.com/TheKorenLab/TIGER. Supplementary information Supplementary data are available at Bioinformatics online

scholarly journals Draft genome sequence data of the facultative, thermophilic, xylanolytic bacterium Paenibacillus sp. strain DA-C8

Data in Brief ◽  
2021 ◽  
Vol 35 ◽  
pp. 106784
Author(s):  
Chinda Chhe ◽  
Ayaka Uke ◽  
Sirilak Baramee ◽  
Umbhorn Ungkulpasvich ◽  
Chakrit Tachaapaikoon ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sequence Data ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Genome Sequence Data ◽  
Paenibacillus Sp

scholarly journals Whole genome sequence data of Mycobacterium tuberculosis XDR strain, isolated from patient in Kazakhstan

Data in Brief ◽  
2020 ◽  
Vol 33 ◽  
pp. 106416
Author(s):  
Asset Daniyarov ◽  
Askhat Molkenov ◽  
Saule Rakhimova ◽  
Ainur Akhmetova ◽  
Zhannur Nurkina ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Genome Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data

scholarly journals Elucidating the genetic basis of an oligogenic birth defect using whole genome sequence data in a non-model organism, Bubalus bubalis

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Lynsey K. Whitacre ◽  
Jesse L. Hoff ◽  
Robert D. Schnabel ◽  
Sara Albarella ◽  
Francesca Ciotola ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Birth Defect ◽  
Genetic Basis ◽  
Sequence Data ◽  
Model Organism ◽  
Bubalus Bubalis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data
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