[Bioperl-l] Nucleotide analysis modules - bugzilla # 1422
redwards at utmem.edu
Sat Jun 21 11:52:00 EDT 2003
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
* 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
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:
The modules etc are available at
If someone could commit them I'd be grateful.
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