| Title |
Pan-Tetris: an interactive visualisation for Pan-genomes
|
|---|---|
| Published in |
BMC Bioinformatics, August 2015
|
| DOI | 10.1186/1471-2105-16-s11-s3 |
| Pubmed ID | |
| Authors |
André Hennig, Jörg Bernhardt, Kay Nieselt |
| Abstract |
Large-scale genome projects have paved the way to microbial pan-genome analyses. Pan-genomes describe the union of all genes shared by all members of the species or taxon under investigation. They offer a framework to assess the genomic diversity of a given collection of individual genomes and moreover they help to consolidate gene predictions and annotations. The computation of pan-genomes is often a challenge, and many techniques that use a global alignment-independent approach run the risk of not separating paralogs from orthologs. Also alignment-based approaches which take the gene neighbourhood into account often need additional manual curation of the results. This is quite time consuming and so far there is no visualisation tool available that offers an interactive GUI for the pan-genome to support curating pan-genomic computations or annotations of orthologous genes. We introduce Pan-Tetris, a Java based interactive software tool that provides a clearly structured and suitable way for the visual inspection of gene occurrences in a pan-genome table. The main features of Pan-Tetris are a standard coordinate based presentation of multiple genomes complemented by easy to use tools compensating for algorithmic weaknesses in the pan-genome generation workflow. We demonstrate an application of Pan-Tetris to the pan-genome of Staphylococcus aureus. Pan-Tetris is currently the only interactive pan-genome visualisation tool. Pan-Tetris is available from http://bit.ly/1vVxYZT. |
X Demographics
The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 77 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| France | 1 | 1% |
| Unknown | 76 | 99% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 23 | 30% |
| Student > Ph. D. Student | 19 | 25% |
| Student > Master | 11 | 14% |
| Student > Bachelor | 8 | 10% |
| Professor > Associate Professor | 3 | 4% |
| Other | 6 | 8% |
| Unknown | 7 | 9% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 26 | 34% |
| Computer Science | 15 | 19% |
| Biochemistry, Genetics and Molecular Biology | 14 | 18% |
| Unspecified | 3 | 4% |
| Psychology | 3 | 4% |
| Other | 8 | 10% |
| Unknown | 8 | 10% |
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 06 April 2018.
All research outputs
#6,961,201
of 22,826,360 outputs
Outputs from BMC Bioinformatics
#2,684
of 7,287 outputs
Outputs of similar age
#81,257
of 264,396 outputs
Outputs of similar age from BMC Bioinformatics
#44
of 117 outputs
Altmetric has tracked 22,826,360 research outputs across all sources so far. This one has received more attention than most of these and is in the 68th percentile.
So far Altmetric has tracked 7,287 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.4. This one has gotten more attention than average, scoring higher than 61% of its peers.
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We're also able to compare this research output to 117 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 60% of its contemporaries.