[Biopython] General question/comment about Bio.Restriction

[Carlos Javier Borroto]

Hi,

We are doing ~100 cloning, and my PI asked me to write a program to
help deciding which enzymes to use and the design of the primers. I
looked and Bio.Restriction has almost everything I had needed until
now, so much that I actually think someone else have been doing
exactly what I'm doing, and because I hate reinventing the wheel, I
wonder if anybody here knows about something that is already public or
could make some comment about.

The program I writing and I almost finished, does this:

1- The program receive a list of proteins ACs, the sequence of the
multi cloning site and the list of possible enzymes to use with the
info of the possibles buffers that they can be use in from the vendor
you are going to use.
2- Using the list of protein ACs, looks into Gene db and from the Gene
entry summary goes and grab the DNA sequence from the genome(I'm
working with hypothetical bacteria proteins, so this is the way I
found to automatize this part, but I don't think is the best, anyway
this is not an important part, you could just give the program your
sequences directly)
3- Iterate through all the sequences doing:
  * grow a pair of forward and reverse primers taking bases from each
end until a set TM is reached(the reverse primer is grown using the
reverse complement of the sequence)
  * Make a restriction analysis using Analysis class with a
RestrictionBatch made out of the list of enzyme given
  * Construct a list of all possible pairs of enzymes from the list of
Ana.without_site().keys(), using the position of the recognition site
of the enzymes in the multi cloning site and what buffer they can be
use in(I need to add temperature also).
  * Save a dictionary with {pair : [list_of_sequence_ids]}
4- select which pair is the one you can use for more sequences
5- remove all the sequences that already have the pair to be use on
them, and repeat from step 3 until all sequences have a pair
6- add the site for the selected enzyme to each primer, adding extra
bases if needed to keep every thing on frame, and also some bases to
avoid pour yield from the digestion with enzymes that doesn't like
cutting near the end.

This program is almost complete, I'm just doing some cleanup and
trying to make it more generic, right now is almost only useful for
this particularly project. I also want to try to make it in to a web
application, let see if my limited coding skills allow me that. But
would be great to hear from other people that may had done something
similar.

I also see that there are stuff like:
>>> from Bio.Restriction import *
>>> EcoRI.buffers.__doc__
'RE.buffers(supplier) -> string.\n\n        not implemented yet.'

I'll love to help finishing work on this, cause it would be very
beneficial for my project, so if I can be pointed in the right
direction, I think I could help.

regards,
-- 
Carlos Javier Borroto
Baltimore, MD
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