Clone mapper: an online suite of tools for RNAi experiments in Caenorhabditis elegans.
Bottom Line: Proper interpretation of results from RNAi experiments requires a series of analytical steps, from the verification of the identity of bacterial clones, to the identification of the clones' potential targets.Despite the popularity of the technique, no user-friendly set of tools allowing these steps to be carried out accurately, automatically, and at a large scale, is currently available.We show that Clone Mapper overcomes the limitations of existing techniques and provide examples illustrating its potential for the identification of biologically relevant genes.
Affiliation: Centre d'Immunologie de Marseille-Luminy, UM2 Aix-Marseille Université, Case 906, 13288 Marseille Cedex 9, France INSERM U1104, 13288 Marseille, France CNRS UMR7280, 13288 Marseille, France.Show MeSH
Mentions: Given the errors that are intrinsic to any large collection of clones, it is indispensable to verify that RNAi clones selected through screens correspond to what they are supposed to be. This is generally done by resequencing and comparing the obtained sequence to the genome of C. elegans and crosschecking the position with that expected for the clone. Checking in this way becomes laborious when one needs to sequence-verify tens or hundreds of clones. We therefore made a BLASTN-based tool to match experimentally determined clone sequences with our in silico clone sequence libraries. It returns an output showing whether the clone is the expected one, and if not what the clone is most likely to be (Figure 3). This became the first tool in a suite that we have called Clone Mapper and for which we provide a web-based access via www.ciml.univ-mrs.fr/EWBANK_jonathan/software.html. The other functionalities are described below.
Affiliation: Centre d'Immunologie de Marseille-Luminy, UM2 Aix-Marseille Université, Case 906, 13288 Marseille Cedex 9, France INSERM U1104, 13288 Marseille, France CNRS UMR7280, 13288 Marseille, France.