OligoFaktorySE is an easy-to-use software for oligonucleotide design. It simplifies the process of designing oligonucleotides and offers a user-friendly interface for creating primers and probes.
The OligoFaktory Standalone Edition is a powerful bioinformatics suite designed to aid researchers in the creation of long oligonucleotides for microarrays, primer pairs for PCR, siRNA, and more. The user interface is designed with ease of use in mind and aims to assist researchers in an automated, reliable, rapid, and painless design process.
The master-detail interface allows users to enter their sequences and related regions with ease. Users may choose to either paste query DNA into the Editor view or use the File > Import… menu item to import FASTA files.
The software offers users the ability to apply several design iterations using five complementary actions. The Design Oligos action enables automated design of long oligonucleotides on an arbitrary number of ORFs, making it an ideal tool for developing DNA microarrays.
Automated design of specific PCR primer pairs on an arbitrary number of regions can be achieved using the Design Primers action. The Design SiRNAs action offers optimal 19bp siRNA design via the method outlined in Rational siRNA design for RNA interference, A. Reynolds et al. Nature biotechnology, 2004, vol 22, 326-330.
Users can identify all repetitions and microsatellites under user-specified constraints by utilizing the Detect Repetitions action. The Merge Regions action merges regions that are too close to allow designing specific primer pairs.
If needed, users can select a species against which oligonucleotide sensitivity and specificity will be evaluated. Results can be visualized in three different formats, including the Hierarchy view, List view, and Statistics view, which summarize results with charts illustrating the distribution of primary features.
Detailed information on heterodimer, hairpin, sensitivity, homodimer, and specificity can be obtained by clicking on the oligonucleotide sequence. Results may be exported to FASTA, a comma-delimited file (CSV) for use with most spreadsheet programs such as Microsoft Excel, or a web archive compatible with Safari.
Overall, OligoFaktory Standalone Edition is an excellent choice for researchers looking for a reliable and easy-to-use bioinformatics suite for the design of long oligonucleotides for microarrays, primer pairs for PCR, siRNA, and more.
The master-detail interface allows users to enter their sequences and related regions with ease. Users may choose to either paste query DNA into the Editor view or use the File > Import… menu item to import FASTA files.
The software offers users the ability to apply several design iterations using five complementary actions. The Design Oligos action enables automated design of long oligonucleotides on an arbitrary number of ORFs, making it an ideal tool for developing DNA microarrays.
Automated design of specific PCR primer pairs on an arbitrary number of regions can be achieved using the Design Primers action. The Design SiRNAs action offers optimal 19bp siRNA design via the method outlined in Rational siRNA design for RNA interference, A. Reynolds et al. Nature biotechnology, 2004, vol 22, 326-330.
Users can identify all repetitions and microsatellites under user-specified constraints by utilizing the Detect Repetitions action. The Merge Regions action merges regions that are too close to allow designing specific primer pairs.
If needed, users can select a species against which oligonucleotide sensitivity and specificity will be evaluated. Results can be visualized in three different formats, including the Hierarchy view, List view, and Statistics view, which summarize results with charts illustrating the distribution of primary features.
Detailed information on heterodimer, hairpin, sensitivity, homodimer, and specificity can be obtained by clicking on the oligonucleotide sequence. Results may be exported to FASTA, a comma-delimited file (CSV) for use with most spreadsheet programs such as Microsoft Excel, or a web archive compatible with Safari.
Overall, OligoFaktory Standalone Edition is an excellent choice for researchers looking for a reliable and easy-to-use bioinformatics suite for the design of long oligonucleotides for microarrays, primer pairs for PCR, siRNA, and more.
What's New
Version 1.2: N/A