Nav: Home

Breakthrough in genome visualization

April 23, 2020

Kadir Dede and Dr. Enno Ohlebusch at Ulm University in Germany have devised a method for constructing pan-genome subgraphs at different granularities without having to wait hours and days on end for the software to process the entire genome. Scientists will now be able to create visualizations of pan-genomes on different scales much more rapidly.

The research article "Dynamic construction in pan-genome structures", was published in De Gruyter's open access journal Open Computer Science.

In order to analyze specific parts of a genome, scientists must be able to "see" the parts they are investigating, and this requires a large amount of processing power and time. The Computational Pan-Genomics Consortium encourages researchers to ensure that all information within a data structure is easily accessible for human eyes by visualization support on different scales. However, a pan-genome graph can have thousands to millions of nodes, which are not very easy for human eyes to visualize.

In an experiment, Dede and Ohlebusch used 10 human genomes and computed a graph that contains part of the large repetitive central exon of the human MUC5AC gene. Formerly, researchers had to create an entire index structure of the genomes, which takes about 8.5 hours and requires 38.5 GB of memory. Using the method developed by Dede and Ohlebusch, the researcher simply has to compute two bit-vectors (on which the construction of the subgraph is based) and the subgraph ? containing the reference path and its ?-neighborhood.

Instead of over eight hours, the software constructed the subgraph (including the computation of the bitvectors, which requires about 10 minutes) in only 24.5 minutes and required 39.6 GB of main memory; the subgraph itself required merely 15 KB of memory.

"Based on solid theory, Dede and Ohlebusch present a new method for the flexible and efficient exploration of suspicious genomic regions, highlighting for example pathogenic genes that distinguish new variants of a virus from all previously known genomes," said Prof. Dr. Jens Stoye, head of the Genome Informatics team, Faculty of Technology, Bielefeld University.

The open access paper can be found here: https://doi.org/10.1515/comp-2020-0018
-end-


De Gruyter

Related Memory Articles:

Previously claimed memory boosting font 'Sans Forgetica' does not actually boost memory
It was previously claimed that the font Sans Forgetica could enhance people's memory for information, however researchers from the University of Warwick and the University of Waikato, New Zealand, have found after carrying out numerous experiments that the font does not enhance memory.
Memory boost with just one look
HRL Laboratories, LLC, researchers have published results showing that targeted transcranial electrical stimulation during slow-wave sleep can improve metamemories of specific episodes by 20% after only one viewing of the episode, compared to controls.
VR is not suited to visual memory?!
Toyohashi university of technology researcher and a research team at Tokyo Denki University have found that virtual reality (VR) may interfere with visual memory.
The genetic signature of memory
Despite their importance in memory, the human cortex and subcortex display a distinct collection of 'gene signatures.' The work recently published in eNeuro increases our understanding of how the brain creates memories and identifies potential genes for further investigation.
How long does memory last? For shape memory alloys, the longer the better
Scientists captured live action details of the phase transitions of shape memory alloys, giving them a better idea how to improve their properties for applications.
A NEAT discovery about memory
UAB researchers say over expression of NEAT1, an noncoding RNA, appears to diminish the ability of older brains to form memories.
Molecular memory can be used to increase the memory capacity of hard disks
Researchers at the University of Jyväskylä have taken part in an international British-Finnish-Chinese collaboration where the first molecule capable of remembering the direction of a magnetic above liquid nitrogen temperatures has been prepared and characterized.
Memory transferred between snails
Memories can be transferred between organisms by extracting ribonucleic acid (RNA) from a trained animal and injecting it into an untrained animal, as demonstrated in a study of sea snails published in eNeuro.
An immunological memory in the brain
Inflammatory reactions can change the brain's immune cells in the long term -- meaning that these cells have an 'immunological memory.' This memory may influence the progression of neurological disorders that occur later in life, and is therefore a previously unknown factor that could influence the severity of these diseases.
Anxiety can help your memory
Anxiety can help people to remember things, a study from the University of Waterloo has found.
More Memory News and Memory Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

Listen Again: Meditations on Loneliness
Original broadcast date: April 24, 2020. We're a social species now living in isolation. But loneliness was a problem well before this era of social distancing. This hour, TED speakers explore how we can live and make peace with loneliness. Guests on the show include author and illustrator Jonny Sun, psychologist Susan Pinker, architect Grace Kim, and writer Suleika Jaouad.
Now Playing: Science for the People

#565 The Great Wide Indoors
We're all spending a bit more time indoors this summer than we probably figured. But did you ever stop to think about why the places we live and work as designed the way they are? And how they could be designed better? We're talking with Emily Anthes about her new book "The Great Indoors: The Surprising Science of how Buildings Shape our Behavior, Health and Happiness".
Now Playing: Radiolab

The Third. A TED Talk.
Jad gives a TED talk about his life as a journalist and how Radiolab has evolved over the years. Here's how TED described it:How do you end a story? Host of Radiolab Jad Abumrad tells how his search for an answer led him home to the mountains of Tennessee, where he met an unexpected teacher: Dolly Parton.Jad Nicholas Abumrad is a Lebanese-American radio host, composer and producer. He is the founder of the syndicated public radio program Radiolab, which is broadcast on over 600 radio stations nationwide and is downloaded more than 120 million times a year as a podcast. He also created More Perfect, a podcast that tells the stories behind the Supreme Court's most famous decisions. And most recently, Dolly Parton's America, a nine-episode podcast exploring the life and times of the iconic country music star. Abumrad has received three Peabody Awards and was named a MacArthur Fellow in 2011.