PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila

<p>Abstract</p> <p>Background</p> <p>The enormous potential of natural variation for the functional characterization of genes has been neglected for a long time. Only since recently, functional geneticists are starting to account for natural variation in their analyses....

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Main Authors: Nolte Viola, Orozco-terWengel Pablo, Kofler Robert, Pandey Ram, Schlötterer Christian
Format: Article
Language:English
Published: BMC 2011-03-01
Series:BMC Genetics
Online Access:http://www.biomedcentral.com/1471-2156/12/27
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spelling doaj-ef2d9a69c9da453e86e2862f0e11f73d2020-11-25T03:10:54ZengBMCBMC Genetics1471-21562011-03-011212710.1186/1471-2156-12-27PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in DrosophilaNolte ViolaOrozco-terWengel PabloKofler RobertPandey RamSchlötterer Christian<p>Abstract</p> <p>Background</p> <p>The enormous potential of natural variation for the functional characterization of genes has been neglected for a long time. Only since recently, functional geneticists are starting to account for natural variation in their analyses. With the new sequencing technologies it has become feasible to collect sequence information for multiple individuals on a genomic scale. In particular sequencing pooled DNA samples has been shown to provide a cost-effective approach for characterizing variation in natural populations. While a range of software tools have been developed for mapping these reads onto a reference genome and extracting SNPs, linking this information to population genetic estimators and functional information still poses a major challenge to many researchers.</p> <p>Results</p> <p>We developed PoPoolation DB a user-friendly integrated database. Popoolation DB links variation in natural populations with functional information, allowing a wide range of researchers to take advantage of population genetic data. PoPoolation DB provides the user with population genetic parameters (Watterson's <it>θ </it>or Tajima's <it>π</it>), Tajima's D, SNPs, allele frequencies and indels in regions of interest. The database can be queried by gene name, chromosomal position, or a user-provided query sequence or GTF file. We anticipate that PoPoolation DB will be a highly versatile tool for functional geneticists as well as evolutionary biologists.</p> <p>Conclusions</p> <p>PoPoolation DB, available at <url>http://www.popoolation.at/pgt</url>, provides an integrated platform for researchers to investigate natural polymorphism and associated functional annotations from UCSC and Flybase genome browsers, population genetic estimators and RNA-seq information.</p> http://www.biomedcentral.com/1471-2156/12/27
collection DOAJ
language English
format Article
sources DOAJ
author Nolte Viola
Orozco-terWengel Pablo
Kofler Robert
Pandey Ram
Schlötterer Christian
spellingShingle Nolte Viola
Orozco-terWengel Pablo
Kofler Robert
Pandey Ram
Schlötterer Christian
PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila
BMC Genetics
author_facet Nolte Viola
Orozco-terWengel Pablo
Kofler Robert
Pandey Ram
Schlötterer Christian
author_sort Nolte Viola
title PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila
title_short PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila
title_full PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila
title_fullStr PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila
title_full_unstemmed PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila
title_sort popoolation db: a user-friendly web-based database for the retrieval of natural polymorphisms in drosophila
publisher BMC
series BMC Genetics
issn 1471-2156
publishDate 2011-03-01
description <p>Abstract</p> <p>Background</p> <p>The enormous potential of natural variation for the functional characterization of genes has been neglected for a long time. Only since recently, functional geneticists are starting to account for natural variation in their analyses. With the new sequencing technologies it has become feasible to collect sequence information for multiple individuals on a genomic scale. In particular sequencing pooled DNA samples has been shown to provide a cost-effective approach for characterizing variation in natural populations. While a range of software tools have been developed for mapping these reads onto a reference genome and extracting SNPs, linking this information to population genetic estimators and functional information still poses a major challenge to many researchers.</p> <p>Results</p> <p>We developed PoPoolation DB a user-friendly integrated database. Popoolation DB links variation in natural populations with functional information, allowing a wide range of researchers to take advantage of population genetic data. PoPoolation DB provides the user with population genetic parameters (Watterson's <it>θ </it>or Tajima's <it>π</it>), Tajima's D, SNPs, allele frequencies and indels in regions of interest. The database can be queried by gene name, chromosomal position, or a user-provided query sequence or GTF file. We anticipate that PoPoolation DB will be a highly versatile tool for functional geneticists as well as evolutionary biologists.</p> <p>Conclusions</p> <p>PoPoolation DB, available at <url>http://www.popoolation.at/pgt</url>, provides an integrated platform for researchers to investigate natural polymorphism and associated functional annotations from UCSC and Flybase genome browsers, population genetic estimators and RNA-seq information.</p>
url http://www.biomedcentral.com/1471-2156/12/27
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AT koflerrobert popoolationdbauserfriendlywebbaseddatabasefortheretrievalofnaturalpolymorphismsindrosophila
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