UniPrime
Overview
UniPrime is an open-source software which automatically designs large sets of universal primers by simply inputting a GeneID reference. UniPrime automatically retrieves and aligns orthologous sequences from GenBank, identifies regions of conservation within the alignment and generates suitable primers that can amplify variable genomic regions. UniPrime differs from previous automatic primer design programs in that all steps of primer design are automated, saved and are phylogenetically limited. We have experimentally verified the efficiency and success of this program. UniPrime is an experimentally validated, fully automated program that generates successful cross-species primers that take into account the biological aspects of the PCR.
The current version is UniPrime 1.18 (Prune / April 2nd, 2008).
Documentation
Text files associated with the UniPrime: README INSTALL LICENSE.
Download
The Linux/Unix code is publicly available.
Before installing UniPrime, your system must be compliant with the following requirements:
- Perl 5.005 or later.
- BioPerl modules: UniPrime uses functionality provided in BioPerl modules.
- Primer3 is mandatory since UniPrime is based on Primer3.
- T-coffee is mandatory if you plan to use multi-alignment option.
- PostgreSQL is mandatory since UniPrime store all the sequences, alignments and primers in a database.
Once you download, uncompress (bunzip2), and un-tar (tar xf), see the file INSTALL for the installation instructions.
Tutorial
Here is a simple example of a full execution of UniPrime. Each step can be reviewed with the web-companion interface. For a complete explanation consult the file README.
1. Added a new locus and use the human OAZ1 gene as prototype. The GeneID (4946) is retrieved from GenBank (from the command line in a Terminal window):
./uniprime.pl --action=locus --target=4946 -v
2. Use the locusID L3.1 (case sensitive) and look for orthologues within the class Mammalia and an e-value of 2e-50 as threshold:
./uniprime.pl --action=ortho --target=L3.1 -e=2e-50 --query=Mammalia[ORGN] -v
3. Use the locusID L3.1 and establish an alignment and a consensus sequence with a threshold of 60%:
./uniprime.pl --action=align --target=L3.1 -c=60 -v
4. Use the locusID L3.1 and design the primer set:
./uniprime.pl --action=primer --target=L3.1 -v
5. Optionally, use the primer set X3.2 and do a virual PCR within the Class Mammalia of the WGS databank of the NCBI.
./uniprime.pl --action=vpcr --target=X3.2 --db=wgs --query=Mammalia[ORGN] -v
Want More?
See the BatLab and Web services.
