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- Introduction
- ORFprimer is a Java Application for automatical primer design. It is based on our previously released software ORFer that reads the GenBank XML- and fasta- sequence
format. Protein sequences are typically downloaded by simply specifying the GI identifier or accession
number of the corresponding protein target. ORFer will extract the open reading frame from the requested protein sequences and display it (see screenshots).
- ORFprimer automatically calculates PCR primers for these sequences. The handling of ORFprimer is intuitional and quite simple using the default settings. In addition it provides many possibilities to change the calculation options before and also after the computation of primers, such as:
- shift of the primers position,
- change of the desired melting temperature,
- change of the restriction sites in the primers sequences.
This way ORFprimer combines convenience and adaptability in one program which makes it a powerful software tool.
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ORFprimer provides a database interface that allows to store the retrieved sequences in a local SQL database. This database can be set up by using the scripts of the ORFprimer installation package. At the moment MySQL, Oracle and Microsoft Access are supported.
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A peer-reviewed paper
on ORFer was published in BMC Bioinformatics
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