scholarly journals VarSome: The Human Genomic Variant Search Engine

2018 ◽  
Author(s):  
Christos Kopanos ◽  
Vasilis Tsiolkas ◽  
Alexandros Kouris ◽  
Charles E. Chapple ◽  
Monica Albarca Aguilera ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Search Engine ◽  
Impact Analysis ◽  
Analysis Tool ◽  
Human Genetic Variation ◽  
Link Type ◽  
Human Genomic ◽  
Genomic Variant ◽  
Global Expertise

AbstractSummaryVarSome.com is a search engine, aggregator and impact analysis tool for human genetic variation and a community-driven project aiming at sharing global expertise on human variants.AvailabilityVarSome is freely available at http://varsome.com.

scholarly journals VarSome: the human genomic variant search engine

2018 ◽  
Vol 35 (11) ◽  
pp. 1978-1980 ◽  
Author(s):  
Christos Kopanos ◽  
Vasilis Tsiolkas ◽  
Alexandros Kouris ◽  
Charles E Chapple ◽  
Monica Albarca Aguilera ◽  
...  
Keyword(s):  
Search Engine ◽  
Human Genomic ◽  
Genomic Variant

scholarly journals Varstation: a complete and efficient tool to support NGS data analysis

2019 ◽  
Author(s):  
ACO Faria ◽  
MP Caraciolo ◽  
RM Minillo ◽  
TF Almeida ◽  
SM Pereira ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Data Analysis ◽  
Supplementary Information ◽  
Human Genetic Variation ◽  
Supplementary Data ◽  
Efficient Tool ◽  
Link Type ◽  
Data Processor ◽  
Ngs Data Analysis ◽  
Ngs Data

AbstractSummaryVarstation is a cloud-based NGS data processor and analyzer for human genetic variation. This resource provides a customizable, centralized, safe and clinically validated environment aiming to improve and optimize the flow of NGS analyses and reports related with clinical and research genetics.Availability and implementationVarstation is freely available at http://varstation.com, for academic [email protected] informationSupplementary data are available at Bioinformatics online.

Revitalizing Difference in the HapMap: Race and Contemporary Human Genetic Variation Research

2008 ◽  
Vol 36 (3) ◽  
pp. 471-477 ◽  
Author(s):  
Jennifer A. Hamilton
Keyword(s):  
Genetic Variation ◽  
Human Genome ◽  
Genetic Research ◽  
The United States ◽  
Genome Project ◽  
Human Genetic Variation ◽  
Early 21St Century ◽  
The Social ◽  
English Speaking ◽  
The Human Genome Project

In 2000, researchers from the Human Genome Project (HGP) proclaimed that the initial sequencing of the human genome definitively proved, among other things, that there was no genetic basis for race. The genetic fact that most humans were 99.9% the same at the level of their DNA was widely heralded and circulated in the English-speaking press, especially in the United States. This pronouncement seemed proof that long-term antiracist efforts to de-biologize race were legitimized by scientific findings. Yet, despite the seemingly widespread acceptance of the social construction of race, post-HGP genetic science has seen a substantial shift toward the use of race variables in genetic research and, according to a number of prominent scholars, is re-invoking the specter of earlier forms of racial science in some rather discomfiting ways. During the past seven years, the main thrust of human genetic research, especially in the realm of biomedicine, has shifted from a concern with the 99.9% of the shared genome — what is thought to make humans alike — towards an explicit focus on the 0.1% that constitutes human genetic variation. Here I briefly explore some of the potential implications of the conceptualization and practice of early 21st century genetic variation research, especially as it relates to questions of race.

scholarly journals RiboA: a web application to identify ribosome A-site locations in ribosome profiling data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Danying Shao ◽  
Nabeel Ahmed ◽  
Nishant Soni ◽  
Edward P. O’Brien
Keyword(s):  
Integer Programming ◽  
Web Application ◽  
Stop Codon ◽  
Ribosome Profiling ◽  
Programming Method ◽  
Analysis Tool ◽  
Site Location ◽  
Link Type ◽  
Wide Range ◽  
A Site

Abstract Background Translation is a fundamental process in gene expression. Ribosome profiling is a method that enables the study of transcriptome-wide translation. A fundamental, technical challenge in analyzing Ribo-Seq data is identifying the A-site location on ribosome-protected mRNA fragments. Identification of the A-site is essential as it is at this location on the ribosome where a codon is translated into an amino acid. Incorrect assignment of a read to the A-site can lead to lower signal-to-noise ratio and loss of correlations necessary to understand the molecular factors influencing translation. Therefore, an easy-to-use and accurate analysis tool is needed to accurately identify the A-site locations. Results We present RiboA, a web application that identifies the most accurate A-site location on a ribosome-protected mRNA fragment and generates the A-site read density profiles. It uses an Integer Programming method that reflects the biological fact that the A-site of actively translating ribosomes is generally located between the second codon and stop codon of a transcript, and utilizes a wide range of mRNA fragment sizes in and around the coding sequence (CDS). The web application is containerized with Docker, and it can be easily ported across platforms. Conclusions The Integer Programming method that RiboA utilizes is the most accurate in identifying the A-site on Ribo-Seq mRNA fragments compared to other methods. RiboA makes it easier for the community to use this method via a user-friendly and portable web application. In addition, RiboA supports reproducible analyses by tracking all the input datasets and parameters, and it provides enhanced visualization to facilitate scientific exploration. RiboA is available as a web service at https://a-site.vmhost.psu.edu/. The code is publicly available at https://github.com/obrien-lab/aip_web_docker under the MIT license.

GENETIC DIVERSITY

PEDIATRICS ◽  
1977 ◽  
Vol 59 (3) ◽  
pp. 432-432
Author(s):  
R. C. Lewontin ◽  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Skin Color ◽  
Human Genetic Variation ◽  
Human Species

Only about 7% of all human genetic diversity is between major races. It would appear then that the superficial characters of skin color, hair form, lip, nose, and eye shape that we use to distinguish human races are atypical and do not represent the mode of human genetic variation. The taxonomic division of the human species into races places a completely disproportionate emphasis on a very small fraction of total human genetic diversity.

An overview of human genetic variation

2018 ◽  
pp. 361-396 ◽  
Author(s):  
Tom Strachan ◽  
Andrew P Read
Keyword(s):  
Genetic Variation ◽  
Human Genetic Variation
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