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Scripts and Applications

ORFprimer

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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.
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 adaptability and convenience in one program which makes it a powerful software tool.
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.
Here are some key features of "ORFprimer":
Simple usage:
· ORFprimer is almost self-explanatory
· The graphical user interface (GUI) simplyfies the handling.
Compatibility:
· ORFprimer was implemented in Java
· ORFprimer is platform independent
· ORFprimer can be executed on different machines: Windows, Linux, Mac, Unix,...
Online accessibility:
· The Java Web Start Technology allows to start ORFprimer via internet
· Explicit download and installation procedure are not necessary.
Data management:
· ORFprimer includes tools to set up your own database.
· Concurrently (MySQL,Oracle and Micosoft Access) are supported.
· Alternatively, the data can be written to files (e.g. fasta format).
High throughput computation:
· ORFprimer can be used to compute primers for up to thousands of target sequences.
· This procedure can be automated furthermore by reading the targets through text files.

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