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X Demographics
Mendeley readers
Attention Score in Context
| Title |
PGAP-X: extension on pan-genome analysis pipeline
|
|---|---|
| Published in |
BMC Genomics, January 2018
|
| DOI | 10.1186/s12864-017-4337-7 |
| Pubmed ID | |
| Authors |
Yongbing Zhao, Chen Sun, Dongyu Zhao, Yadong Zhang, Yang You, Xinmiao Jia, Junhui Yang, Lingping Wang, Jinyue Wang, Haohuan Fu, Yu Kang, Fei Chen, Jun Yu, Jiayan Wu, Jingfa Xiao |
| Abstract |
Since PGAP (pan-genome analysis pipeline) was published in 2012, it has been widely employed in bacterial genomics research. Though PGAP has integrated several modules for pan-genomics analysis, how to properly and effectively interpret and visualize the results data is still a challenge. To well present bacterial genomic characteristics, a novel cross-platform software was developed, named PGAP-X. Four kinds of data analysis modules were developed and integrated: whole genome sequences alignment, orthologous genes clustering, pan-genome profile analysis, and genetic variants analysis. The results from these analyses can be directly visualized in PGAP-X. The modules for data visualization in PGAP-X include: comparison of genome structure, gene distribution by conservation, pan-genome profile curve and variation on genic and genomic region. Meanwhile, result data produced by other programs with similar function can be imported to be further analyzed and visualized in PGAP-X. To test the performance of PGAP-X, we comprehensively analyzed 14 Streptococcus pneumonia strains and 14 Chlamydia trachomatis. The results show that, S. pneumonia strains have higher diversity on genome structure and gene contents than C. trachomatis strains. In addition, S. pneumonia strains might have suffered many evolutionary events, such genomic rearrangements, frequent horizontal gene transfer, homologous recombination, and other evolutionary process. Briefly, PGAP-X directly presents the characteristics of bacterial genomic diversity with different visualization methods, which could help us to intuitively understand dynamics and evolution in bacterial genomes. The source code and the pre-complied executable programs are freely available from http://pgapx.ybzhao.com . |
X Demographics
The data shown below were collected from the profiles of 2 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| France | 1 | 50% |
| Unknown | 1 | 50% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 1 | 50% |
| Members of the public | 1 | 50% |
Mendeley readers
The data shown below were compiled from readership statistics for 85 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 85 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 12 | 14% |
| Student > Master | 12 | 14% |
| Researcher | 10 | 12% |
| Student > Bachelor | 9 | 11% |
| Student > Doctoral Student | 9 | 11% |
| Other | 16 | 19% |
| Unknown | 17 | 20% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 26 | 31% |
| Biochemistry, Genetics and Molecular Biology | 19 | 22% |
| Computer Science | 4 | 5% |
| Immunology and Microbiology | 3 | 4% |
| Engineering | 3 | 4% |
| Other | 6 | 7% |
| Unknown | 24 | 28% |
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
#6,491,526
of 23,018,998 outputs
Outputs from BMC Genomics
#2,905
of 10,697 outputs
Outputs of similar age
#133,843
of 441,339 outputs
Outputs of similar age from BMC Genomics
#66
of 208 outputs
Altmetric has tracked 23,018,998 research outputs across all sources so far. This one has received more attention than most of these and is in the 70th percentile.
So far Altmetric has tracked 10,697 research outputs from this source. They receive a mean Attention Score of 4.7. This one has gotten more attention than average, scoring higher than 71% 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 441,339 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 68% of its contemporaries.
We're also able to compare this research output to 208 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 67% of its contemporaries.