[Bioperl-l] Nucleotide analysis modules - bugzilla # 1422

[Rob Edwards]

I have written a bunch of nucleotide analysis and manipulation modules that 
I'd like someone to commit to the CVS for me.

The modules are:
    * Bio/Seq/PrimedSeq.pm - a sequence object containing two primers
    * Bio/SeqFeature/Primer.pm - a representation of a single primer
    * Bio/Tools/Analysis/Nucleotide/Clone.pm - "clone" DNA and move sequence 
features around
    * Bio/Tools/Analysis/Nucleotide/PCRSimulation.pm - simulate PCR
    * Bio/Tools/Analysis/Nucleotide/Primer3.pm - analyze primer3 output 
    * Bio/Tools/Analysis/Nucleotide/Restriction/Enzyme.pm - a representation 
of a single restriction enzyme
    * Bio/Tools/Analysis/Nucleotide/Restriction/EnzymeCollection.pm - a 
representation of a bunch of enzymes
    * Bio/Tools/Analysis/Nucleotide/RestrictionAnalysis.pm - analyze 
restriction sites in a DNA sequence
    * Bio/Tools/Run/Primer3.pm - run the Primer3 program. 

Some of these are based on a lot of work by others, and I have enhanced them. 
In particular Bio/Tools/Analysis/Nucleotide/RestrictionAnalysis.pm should 
replace Bio/Tools/RestrictionEnzyme.pm. The new module contains all that 
functionality and has been extended to deal properly with redundant sequences 
and with Bio/Tools/Analysis/Nucleotide/Restriction/EnzymeCollection.pm rebase 
files can be parsed.

I tried to write the pod to be compliant with the Pod Gods, and ran 
maintenance/pod.pl -d Bio -v -b on these scripts - that should give me any 
errors, right?

In addition to the modules and test scripts there are a couple of examples 
that will let you run primer3 to design primers, cut DNA with restriction 
enzymes, and perform PCR and clone genes.

Some of these modules address the bugs in bugzilla 1422: 
http://bugzilla.bioperl.org/show_bug.cgi?id=1422

The modules etc are available at 
http://www.salmonella.org/bioperl/nucleotide_analyses.tgz

If someone could commit them I'd be grateful.

Thanks

Rob