GEAR: The Genome Analysis Server Eases Wet-Lab Data Analysis

Andreas Untergasser
Tobias Rausch1, Markus Hsi-Yang Fritz2, Vladimir Benes1, Andreas Untergasser1,3
1) European Molecular Biology Laboratory, Genomics Core Facility, Heidelberg, Germany;
2) European Molecular Biology Laboratory, Genome Biology Unit, EMBL, Heidelberg, Germany;
3) Heidelberg University, Heidelberg, Germany;

The genome analysis server (GEAR: is a wide collection of tools supporting molecular biologists in everyday lab tasks. An enhanced version of Primer3Plus allows the selection of primers for many use cases like detection, qPCR, cloning and sequencing. Secondary structures are now also drawn and can be evaluated by the researcher. Silica can perform in-silico PCRs on a selected genome with a set of provided primers. It localizes primer binding sites and calculates the amplicons. The Wily-DNA-Editor is a DNA sequence editor supporting genbank files and sufficient for common plasmid manipulation tasks. Users can edit or reverse complement the sequence, find restriction sites, draw restriction maps, calculate digests, find open reading frames, translate sequences and allows a custom feature annotation. Due to its JavaScript nature all data are processed in the user’s browser without being transferred to the server. Teal, Sage and Indigo display Sanger trace files and extract the sequence information. They ease the evaluation by aligning the trace file to a genome or a provided reference sequence highlighting the found differences. Last, the RDML tools support users in the evaluation and the padding of RDML files. The user can validate the files against the schema format description, fix common errors and build RDML files from table data. Ultimately, the RDML tools will allow to edit and analyze RDML files as well as evaluating compliance with MIQE. These tools are very useful for molecular biologists as they solve common lab tasks and enable to work at any computer with internet connection and a current browser – without the need of installing software locally. The code is open source and users that due to legal restrictions cannot send their data on servers over the internet may opt to install an own version of gear on a local server and process their data in house. Digital PCR provides new challenges. The RDML format has to be extended to support dPCR data in an efficient way and the tools have to be extended to visualize the data. Last, we would like to draw attention to a session on RDML and digital PCR were everybody is invited to provide suggestions on the further development of RDML.

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