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

[Hilmar Lapp]

This stuff sounds very useful Rob. Would you be willing to commit this 
yourself if we set you up with a CVS write account? Chris, if you read 
this and you have a minute, could you set him up?

The long path is intimidating, but the naming makes sense. What do 
others feel? I'm afraid Jason and Ewan are looking at other things 
right now than their email ... If there is a single entry module for 
the user, and <...>/RestrictionAnalysis.pm looks sounds like it could 
be that, my suggestion would be to put that into Bio::Tools so that 
people don't have too hard of a time finding it.

	-hilmar

On Saturday, June 21, 2003, at 08:52  AM, Rob Edwards wrote:

> 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
>
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>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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