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OligoFaktorySE - Oligonucleotide design made simple OligoFaktory Standalone Edition is an integrated suite of bioinformatics tools for the design of long oligonucleotide for micro-array, of primer pair for PCR, of siRNA and more. The user interface emphasizes useability and is aimed at assisting researchers for a painless, rapid, automated, and reliable design.A master-detail interface allow users to enter their sequences and related regions. Users can cut-and-paste query DNA into the Editor view, or they can use the File > Import menu item to import FASTA files.Several design iterations can be applied, using five complementary actions:· The Design Oligos action allows for the automated design of specific long oligonucleotides on an arbitrary number of ORFs (e.g., for the development of DNA microarrays).· The Design Primers action allows for the automated design of specific PCR primer pairs on an arbitrary number of regions.· The Design SiRNAs action allows designing optimal 19bp siRNA with the method described in Rational siRNA design for RNA interference, A. Reynolds et al. Nature biotechnology, 2004, vol 22, 326-330.· The Detect Repetitions action identifies all repetitions and microsatelites under user-specified constraints.· The Merge Regions action merges regions which are too close to allow designing specific primer pairs.If needed, you can choose a species against which oligonucleotide sensitivity and specificity will be evaluated.· You will be able to visualize your results in three different flavours:· The Hierarchy view is a long listing that shows relative location bargraphs of queries and results.· The List view is a short listing that emphasizes leaf results, while hiding locations information.· The Statistics view summarizes the results with charts showing the distributions of main features.All detailed information on heterodimer, hairpin, sensitivity, homodimer, and specificity are obtained by clicking on the oligonucleotide sequence.You can export results to FASTA or a comma delimited file (CSV), readable by most spreadsheet programs such as Microsoft Excel. You can also export the current view to a web archive compatible with Safari. What's New in This Release: · The look and feel of the user interface and the undo/redo behaviors are improved.

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