How do I find all the ORFs in a nucleotide seque...
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How do I find all the ORFs in a nucleotide sequence? Antigenic sites in a protein? Calculate nucleotide melting temperature? Find repeats?
In fact, none of these functions are built into BioPerl but they are all available in the EMBOSS package, as well as many others. The BioPerl developers created a simple interface to EMBOSS such that any and all EMBOSS programs can be run from within BioPerl. See Bio::Factory::EMBOSS for more information, it's in the bioperl-run package.
If you can't find the functionality you want in BioPerl then make sure to look for it in EMBOSS, these packages integrate quite gracefully with BioPerl. Of course, you will have to install EMBOSS to get this functionality.
In addition, BioPerl after version 1.0.1 contains the Pise/Bioperl modules. The Pise package was designed to provide a uniform interface to bioinformatics applications, and currently provides wrappers to greater than 250 such applications! Included amongst these wrapped apps are HMMER, PHYLIP, BLAST, GENSCAN, and the EMBOSS suite. Use of the Pise/BioPerl modules does not require installation of Pise locally as it runs through the HTTP protocol of the web. Also, see the BioMOBY project for information on running applications remotely.
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