PoPoolation DB: A Database for Natural Polymorphisms in Drosophila
Author Information
Author(s): Pandey Ram Vinay, Kofler Robert, Orozco-ter Wengel Pablo, Nolte Viola, Schlötterer Christian
Primary Institution: Institut für Populationsgenetik, Vetmeduni Vienna
Conclusion
PoPoolation DB provides an integrated platform for researchers to investigate natural polymorphism and associated functional annotations.
Supporting Evidence
- PoPoolation DB links variation in natural populations with functional information.
- The database can be queried by gene name, chromosomal position, or a user-provided query sequence.
- PoPoolation DB provides population genetic parameters such as Watterson's θ and Tajima's π.
- It allows users to visualize population genetic data along with functional annotations.
- Natural variation is measured by pairwise sequence comparisons and the number of segregating sites.
Takeaway
PoPoolation DB is a tool that helps scientists find genetic differences in fruit flies by using data from many flies at once.
Methodology
The database was developed using MySQL and Perl, and it allows users to query genetic data by gene name, chromosomal position, or custom sequences.
Limitations
PoPoolation DB is restricted to the analysis of Illumina sequence reads generated from pooled DNA samples.
Participant Demographics
The study involved a pool of flies consisting of five females from each of 113 isofemale lines collected in Northern Portugal.
Digital Object Identifier (DOI)
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