algorithm

Another technique used to build restriction maps leads to the Probed Partial Digest problem (PPDP). In this method DNA is partially digested with a re- striction enzyme, thus generating a collection of DNA fragments between every two cutting sites. After this, a labeled probe that attaches to the DNA be- tween two cutting sites is hybridized to the partially digested DNA, and the sizes of fragments to which the probe hybridizes are measured. In contrast to the PDP, where the input consists of all partial fragments, the input for the PPDP consists of all partial fragments that contain a given point (this point corresponds to the position of the labeled probe). The problem is to reconstruct the positions of the sites from the multiset of measured lengths. In the PPDP, we assume that the labeled probe is hybridized at position 0 and that A is the set of restriction sites with negative coordinates while B is the set of restriction sites with positive coordinates. The probed partial digest experiment provides the multiset {b − a : a ∈ A, b ∈ B} and the problem is to find A and B given this set. Implement a brute force algorithm for the PPDP and add a branch-and- bound approach to improve its performance

## Deliverables

1) Complete and fully-functional working program(s) in executable form as well as complete source code of all work done.

2) Deliverables must be in ready-to-run condition, as follows? (depending on the nature? of the deliverables):

a)? For web sites or? other server-side deliverables intended to only ever exist in one place in the Buyer's environment--Deliverables must be installed by the Seller in ready-to-run condition in the Buyer's environment.

b) For all others including desktop software or software the buyer intends to distribute: A software? installation package that will install the software in ready-to-run condition on the platform(s) specified in this bid request.

3) All deliverables will be considered "work made for hire" under U.S. Copyright law. Buyer will receive exclusive and complete copyrights to all work purchased. (No GPL, GNU, 3rd party components, etc. unless all copyright ramifications are explained AND AGREED TO by the buyer on the site per the coder's Seller Legal Agreement).

## Platform

windows

Odd Jobs

Project ID: #3376705

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