THREaD Mapper Studio: A novel, visual web server for the estimation of genetic linkage maps

Jitender Cheema, T. H.Noel Ellis, Jo Dicks*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)

Abstract

The estimation of genetic linkage maps is a key component in plant and animal research, providing both an indication of the genetic structure of an organism and a mechanism for identifying candidate genes associated with traits of interest. Because of this importance, several computational solutions to genetic map estimation exist, mostly implemented as stand-alone software packages. However, the estimation process is often largely hidden from the user. Consequently, problems such as a program crashing may occur that leave a user baffled. THREaD Mapper Studio (http://cbr.jic.ac.uk/threadmapper) is a new web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers. The rationale behind the web site is to make the estimation process as transparent and robust as possible, while also allowing users to use their expert knowledge during analysis. Indeed, the 3D visual nature of the tool allows users to spot features in a data set, such as outlying markers and potential structural rearrangements that could cause problems with the estimation procedure and to account for them in their analysis. Furthermore, THREaD Mapper Studio facilitates the visual comparison of genetic map solutions from third party software, aiding users in developing robust solutions for their data sets.

Original languageEnglish
Article numbergkq430
Pages (from-to)W188-W193
JournalNucleic Acids Research
Volume38
Issue numberSUPPL. 2
DOIs
Publication statusPublished - 21 May 2010
Externally publishedYes

Bibliographical note

Funding Information:
European Union Framework VI Grain Legumes Integrated Project (FOOD-CT-2004-506223); Biotechnology and Biological Sciences Research Council (John Innes Centre Core Strategic Grant). Funding for open access charge: Biotechnology and Biological Sciences Research Council.

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