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

• Published in: Nucleic acids research Vol. 38; no. Web Server issue; pp. W188 - W193
• Main Authors: Cheema, Jitender, Ellis, T.H. Noel, Dicks, Jo
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.07.2010
• Subjects: Chromosome Mapping; Computational Biology; Computer Graphics; Genetic Linkage; Internet; Software
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkq430

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.