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Mendeley readers
Attention Score in Context
| Title |
cFinder: definition and quantification of multiple haplotypes in a mixed sample
|
|---|---|
| Published in |
BMC Research Notes, September 2015
|
| DOI | 10.1186/s13104-015-1382-7 |
| Pubmed ID | |
| Authors |
Norbert Niklas, Julia Hafenscher, Agnes Barna, Karin Wiesinger, Johannes Pröll, Stephan Dreiseitl, Sandra Preuner-Stix, Peter Valent, Thomas Lion, Christian Gabriel |
| Abstract |
Next-generation sequencing allows for determining the genetic composition of a mixed sample. For instance, when performing resistance testing for BCR-ABL1 it is necessary to identify clones and define compound mutations; together with an exact quantification this may complement diagnosis and therapy decisions with additional information. Moreover, that applies not only to oncological issues but also determination of viral, bacterial or fungal infection. The efforts to retrieve multiple haplotypes (more than two) and proportion information from data with conventional software are difficult, cumbersome and demand multiple manual steps. Therefore, we developed a tool called cFinder that is capable of automatic detection of haplotypes and their accurate quantification within one sample. BCR-ABL1 samples containing multiple clones were used for testing and our cFinder could identify all previously found clones together with their abundance and even refine some results. Additionally, reads were simulated using GemSIM with multiple haplotypes, the detection was very close to linear (R(2) = 0.96). Our aim is not to deduce haploblocks over statistics, but to characterize one sample's composition precisely. As a result the cFinder reports the connections of variants (haplotypes) with their readcount and relative occurrence (percentage). Download is available at http://sourceforge.net/projects/cfinder/ . Our cFinder is implemented in an efficient algorithm that can be run on a low-performance desktop computer. Furthermore, it considers paired-end information (if available) and is generally open for any current next-generation sequencing technology and alignment strategy. To our knowledge, this is the first software that enables researchers without extensive bioinformatic support to designate multiple haplotypes and how they constitute to a sample. |
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 % |
|---|---|---|
| Israel | 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 12 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 12 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Bachelor | 2 | 17% |
| Other | 1 | 8% |
| Student > Doctoral Student | 1 | 8% |
| Student > Ph. D. Student | 1 | 8% |
| Student > Master | 1 | 8% |
| Other | 2 | 17% |
| Unknown | 4 | 33% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 2 | 17% |
| Engineering | 2 | 17% |
| Computer Science | 1 | 8% |
| Medicine and Dentistry | 1 | 8% |
| Immunology and Microbiology | 1 | 8% |
| Other | 0 | 0% |
| Unknown | 5 | 42% |
Attention Score in Context
This research output has an Altmetric Attention Score of 1. 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 21 September 2015.
All research outputs
#15,329,366
of 23,577,761 outputs
Outputs from BMC Research Notes
#2,153
of 4,305 outputs
Outputs of similar age
#149,948
of 269,154 outputs
Outputs of similar age from BMC Research Notes
#91
of 173 outputs
Altmetric has tracked 23,577,761 research outputs across all sources so far. This one is in the 32nd percentile – i.e., 32% of other outputs scored the same or lower than it.
So far Altmetric has tracked 4,305 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.7. This one is in the 45th percentile – i.e., 45% of its peers scored the same or lower than it.
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We're also able to compare this research output to 173 others from the same source and published within six weeks on either side of this one. This one is in the 45th percentile – i.e., 45% of its contemporaries scored the same or lower than it.