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Team:UPO-Sevilla/Project/Improving Flip Flop/Bioinformatics/Tags Finder
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Latest revision as of 22:21, 27 October 2011
Tags Finder
Goal
To develop a simple Perl program to search a desired tag protein sequence in a query proteome.
Background
When working with proteases, it is essential to make sure that these proteases are going to degrade only their target proteins, so previous studies must be carried out to get rid of possible unwanted endogenous protease targets. In our case, before starting the web lab experiments, we checked that E.coli’s proteome (our model organism) did not show any of the protease ClpXP degradation tags.
Strategy
Perl is an open source programming language which is used extensively in Bioinformatics. We wrote a Perl program to search in E.coli’s proteome all the known ClpXP protease degradation tags. By using this software, the user can choose which ClpXP protease known degradation tag wants to search in a desired proteome. The software comes with all the proteomes of the currently used organisms in synthetic biology downloaded from the NCBI.
Results
This software can be downloaded here.
Sponsors
