| Title |
TRAVeLer: a tool for template-based RNA secondary structure visualization
|
|---|---|
| Published in |
BMC Bioinformatics, November 2017
|
| DOI | 10.1186/s12859-017-1885-4 |
| Pubmed ID | |
| Authors |
Richard Elias, David Hoksza |
| Abstract |
Visualization of RNA secondary structures is a complex task, and, especially in the case of large RNA structures where the expected layout is largely habitual, the existing visualization tools often fail to produce suitable visualizations. This led us to the idea to use existing layouts as templates for the visualization of new RNAs similarly to how templates are used in homology-based structure prediction. This article introduces Traveler, a software tool enabling visualization of a target RNA secondary structure using an existing layout of a sufficiently similar RNA structure as a template. Traveler is based on an algorithm which converts the target and template structures into corresponding tree representations and utilizes tree edit distance coupled with layout modification operations to transform the template layout into the target one. Traveler thus accepts a pair of secondary structures and a template layout and outputs a layout for the target structure. Traveler is a command-line open source tool able to quickly generate layouts for even the largest RNA structures in the presence of a sufficiently similar layout. It is available at http://github.com/davidhoksza/traveler . |
X Demographics
The data shown below were collected from the profiles of 7 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Hong Kong | 1 | 14% |
| Germany | 1 | 14% |
| United Kingdom | 1 | 14% |
| Canada | 1 | 14% |
| Unknown | 3 | 43% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 5 | 71% |
| Members of the public | 2 | 29% |
Mendeley readers
The data shown below were compiled from readership statistics for 18 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 18 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 8 | 44% |
| Student > Ph. D. Student | 3 | 17% |
| Professor | 2 | 11% |
| Professor > Associate Professor | 2 | 11% |
| Student > Doctoral Student | 1 | 6% |
| Other | 0 | 0% |
| Unknown | 2 | 11% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 5 | 28% |
| Computer Science | 5 | 28% |
| Agricultural and Biological Sciences | 3 | 17% |
| Medicine and Dentistry | 2 | 11% |
| Physics and Astronomy | 1 | 6% |
| Other | 0 | 0% |
| Unknown | 2 | 11% |
Attention Score in Context
This research output has an Altmetric Attention Score of 4. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 22 November 2017.
All research outputs
#7,061,424
of 23,571,271 outputs
Outputs from BMC Bioinformatics
#2,646
of 7,395 outputs
Outputs of similar age
#111,451
of 325,972 outputs
Outputs of similar age from BMC Bioinformatics
#49
of 157 outputs
Altmetric has tracked 23,571,271 research outputs across all sources so far. This one has received more attention than most of these and is in the 69th percentile.
So far Altmetric has tracked 7,395 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.5. This one has gotten more attention than average, scoring higher than 63% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 325,972 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 65% of its contemporaries.
We're also able to compare this research output to 157 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 69% of its contemporaries.