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X Demographics
Mendeley readers
Attention Score in Context
| Title |
pSTR Finder: a rapid method to discover polymorphic short tandem repeat markers from whole-genome sequences
|
|---|---|
| Published in |
Investigative Genetics, August 2015
|
| DOI | 10.1186/s13323-015-0027-x |
| Pubmed ID | |
| Authors |
James Chun-I Lee, Bill Tseng, Bing-Ching Ho, Adrian Linacre |
| Abstract |
Whole-genome sequencing is performed routinely as a means to identify polymorphic genetic loci such as short tandem repeat loci. We have developed a simple tool, called pSTR Finder, which is freely available as a means of identifying putative polymorphic short tandem repeat (STR) loci from data generated from genome-wide sequences. The program performs cross comparisons on the STR sequences generated using the Tandem Repeats Finder based on multiple-genome samples in a FASTA format. These comparisons generate reports listing identical, polymorphic, and different STR loci when comparing two samples. The web site http://forensic.mc.ntu.edu.tw:9000/PSTRWeb/Default has been developed as a means to identify polymorphic STR loci within complex mass genome sequences. The program was developed to generate a series of user-friendly reports. As proof of concept for the program, four FASTA genome sequence samples of human chromosome X (AC_000155.1, CM000685.1, NC_018934.2, and CM000274.1) were obtained from GenBank and were analyzed for the presence of putative STR regions. The sequences within AC-000155.1 were used as an initial reference sequence from which there were 5443 identical and 4305 polymorphic STR loci identified using a repeat unit of 1-6 and 10 bp as the flanking sequence either side of the putative STR loci. A reliability test was used to compare five FASTA samples, which had sections of DNA sequence removed to mimic partial or fragmented DNA sequences, to determine whether pSTR Finder can efficiently and consistently find identical, polymorphic, and different STR loci. From the mass of DNA sequence data, the project was found to reproducibly identify polymorphic STR loci and generate user-friendly reports detailing the number and location of these potential polymorphic loci. This freely available program was found to be a useful tool to find polymorphic STR within whole-genome sequence data in forensic genetic studies. |
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 % |
|---|---|---|
| United Kingdom | 1 | 50% |
| Unknown | 1 | 50% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 2 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 21 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 21 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 4 | 19% |
| Student > Bachelor | 3 | 14% |
| Student > Master | 3 | 14% |
| Researcher | 3 | 14% |
| Professor | 1 | 5% |
| Other | 3 | 14% |
| Unknown | 4 | 19% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 9 | 43% |
| Agricultural and Biological Sciences | 5 | 24% |
| Environmental Science | 1 | 5% |
| Unknown | 6 | 29% |
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 06 August 2015.
All research outputs
#18,422,065
of 22,821,814 outputs
Outputs from Investigative Genetics
#87
of 97 outputs
Outputs of similar age
#189,931
of 264,147 outputs
Outputs of similar age from Investigative Genetics
#3
of 3 outputs
Altmetric has tracked 22,821,814 research outputs across all sources so far. This one is in the 11th percentile – i.e., 11% of other outputs scored the same or lower than it.
So far Altmetric has tracked 97 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 21.2. This one is in the 3rd percentile – i.e., 3% of its peers scored the same or lower than it.
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We're also able to compare this research output to 3 others from the same source and published within six weeks on either side of this one.