This module retrieves a BLINK result from NCBI.
This is something I needed for what I was doing. The result is decidedly un-bioperl like, but it works
This module finds repeats in sequences. It will find direct and indirect, and perfect and imperfect repeats.
The module is not necessarily optimized for speed! The imperfect repeat part of it, especially, is really slow because it looks through all the perfect repeats and joins nearby ones together. However it works, and I have used it for sequences > 100kb, and repeats down to 7bp.
The "imperfect repeat" part of it just joins other repeats, so it will find AAAAAAAGAAAAAAA and AAAAAAACAAAAAAA but not AAAAAAAGAA and AAAAAAACAA
The best way to use it is to pass in a Genbank sequence and you'll get a GenBank sequence back with the repeats annotated.
Note: at the moment this module requires Tie::HashRef so that you can have references to hashes as keys and values of hashes. This is really only needed (in the current implementation) for the imperfect repeats.
All the modules have been combined into a single tarball.
The modules are:
There are also test scripts and a couple of example scripts
OK, so there is not much here. First, here are the primer modules that I have been working on.
This version has minor changes from v0.2. The most significant change is that the ePCR module was changed to PCRSimulation.pm because of a conflict with names. Besides, I didn't like ePCR anyway!. Also I have started construction of a Bio::SeqFeature::Generic object so that the primers are returned as an annotated sequence. This allows you to (for example) print out a genbank format file with the sequence and the primers. This works, but I think it keeps adding all the primers, one after another.
This version has substantial changes. The PrimedSeq.pm and Primer.pm modules are largely unchanged, but there are now two Primer3 modules: Bio::Tools::Primer3 to parse Primer3 output and Bio::Tools::Run::Primer3 to run primer3. In addition I have written another module Bio::Tools::ePCR to return Bio::Seq objects representing an amplified sequence. You can supply two primers and a sequence and get the amplified region back. Also, this module finds the ends of the primers so you can add restriction sites and whatnot on the 5' end of a primer and still get an amplified sequence back. There are more examples and test sequences too. Read the README file.
Next, there is version 0.3 of Bio::Tools::Analysis::Nucleotide::RestrictionEnzyme. This version contains several updates from the previous version (0.1):
There is an initial version of Bio::Tools::Analysis::Nucleotide::RestrictionEnzyme suite that I have been messing with. This is based on some bugzilla comments from Heikki Lehvaslaiho and Steve Chervitz. This sort of came together out of some other things I was messing with (rebase) and so I am not sure how good it is. There are three components:
The tarball above contains 4 example scripts that take a sequence, generate some data, and spit out some results.
Large parts of these modules are just rearranged from Steve's early work, and he deserves and gets all the credit for that. I added a few things to make Heikki happy!
As per Heikki's suggestion, I called this suite Bio::Tools::Analysis::Nucleotide::RestrictionEnzyme which is damn long to type all the time, but it should, therefore still play with Bio::Tools::RestrictionEnzyme.
I have put v0.3 of the hackers guide to bioperl online. Not really a guide, more a useful list.
There are some scripts that I have written here