Abstract

Live Cell Array (LCA) technology allows the acquisition of high-resolution time-course profiles of bacterial gene expression by the systematic assessment of fluorescence in living cells carrying either transcriptional or translational fluorescent protein fusion. However, the direct estimation of promoter activities by time-dependent derivation of the fluorescence datasets generates high levels of noise. Here, we present BasyLiCA, a user-friendly open-source interface and database dedicated to the automatic storage and standardized treatment of LCA data. Data quality reports are generated automatically. Growth rates and promoter activities are calculated by tunable discrete Kalman filters that can be set to incorporate data from biological replicates, significantly reducing the impact of noise measurement in activity estimations.
AVAILABILITY: The BasyLiCA software and the related documentation are available at http://genome.jouy.inra.fr/basylica.

Links

Publisher Full Text

Authors

Aïchaoui L, Jules M, Le Chat L, Aymerich S, Fromion V, Goelzer A

Institution

INRA, UR1077 Unité Mathématique Informatique et Génome, F-78350 Jouy en Josas, France.

Source

Bioinformatics (Oxford, England) 28:20 2012 Oct 15 pg 2705-6

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

22764159