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Building Gene Homologs Web Services

Student: 
Ian Archibald

An important way of understanding genetic diseases in humans is to perform research on animal models, such as mice. Unfortunately, mapping genes from one species to another is not straightforward. Some data are available to map genes from one species to another, but where these data do not exist, other approaches are required. This could involve running so called blast queries to determine the most likely candidates.

In an attempt to provide a link between the mouse and human that can be used in several tools, the goal of this project is to provide a number of web services. Where each successive web service allows more detailed control of the mapping process. Those web services will then be incorporated in a number of workflows to allow biologists to perform queries and analysis across species. Setting up the workflows themselves is a bonus assignment if time permits.

Project status: 
Finished
Degree level: 
MSc
Background: 
This requires a person that is willing to search for information on its own and is willing to communicate with domain experts (i.e., bioinformaticians and biologists). You will need to program the web services and deploy these in Tomcat. Moreover, you will need to call other web services to perform the more advanced methods of linking.
Supervisors @ NeSC: 
Other supervisors: 
Richard Baldock (Human Genetics Unit, MRC)
Subject areas: 
Bioinformatics
Databases
Other
Software Engineering
References: 
The Edinburgh Mouse Atlas (EMAGE) http://genex.hgu.mrc.ac.uk/ The human equivalent of EMAGE, the Electronic Atlas of the Developing Human Brain: http://www.ncl.ac.uk/ihg/EADHB/ What does homology means in the context of genes: http://en.wikipedia.org/wiki/Homology_%28biology%29#Homology_of_sequences_in_genetics An example of a web page to search for homolog genes http://bioinfo.cnio.es/cgi-bin/db/homologene
Student project type: