IEEE Transactions on Computational Biology and Bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) is a bimonthly journal that publishes archival research results related to the algorithmic, mathematical, statistical, and computational methods that are central in bioinformatics and computational biology. Read the full scope of TCBB


IEEE Transactions on Computational Biology and Bioinformatics (TCBB) will move to the OnlinePlus publication model starting with 2015 issues!


From the July/August 2015 Issue

Divide and Conquer Approach to Contact Map Overlap Problem Using 2D-Pattern Mining of Protein Contact Networks

By Suvarna Vani Koneru and Durga Bhavani S

Featured article thumbnail imageA novel approach to Contact Map Overlap (CMO) problem is proposed using the two dimensional clusters present in the contact maps. Each protein is represented as a set of the non-trivial clusters of contacts extracted from its contact map. The approach involves finding matching regions between the two contact maps using approximate 2D-pattern matching algorithm and dynamic programming technique. These matched pairs of small contact maps are submitted in parallel to a fast heuristic CMO algorithm. The approach facilitates parallelization at this level since all the pairs of contact maps can be submitted to the algorithm in parallel. Then, a merge algorithm is used in order to obtain the overall alignment. As a proof of concept, MSVNS, a heuristic CMO algorithm is used for global as well as local alignment. The divide and conquer approach is evaluated for two benchmark data sets that of Skolnick and Ding et al. It is interesting to note that along with achieving saving of time, better overlap is also obtained for certain protein folds.

download PDF View the PDF of this article      csdl View this issue in the digital library


Editorials and Announcements

Announcements

  • Get Your Journals as eBooks for Free

  • TCBB celebrates its 10th Anniversary. Editor-in-Chief Ying Xu says, "The emergence and maturation of increasingly more and powerful molecular measurement technologies such as next generation sequencing and chromosome conformation capture allow scientists to tackle biological problems at the depth and breadth that we have never seen before. At the same time the enormity and complexity of the data generated using these technologies raised tremendous challenges to computational scientists to develop more effective techniques to store, transmit, organize, process, analyze and mine the data, and to construct models to assist interpreting the data. Since its creation ten years ago, TCBB has been playing a major role in bridging the world of computing and the world of biology. I want to congratulate what the journal has done in providing biologists with the most powerful computational tools to help address their data and modeling needs. I fully expect that TCBB will continue to play increasingly significant roles in attracting more computational scientists to address the ever increasing needs for new and more powerful computational techniques and to introduce to new comers the important and challenging computational biology problems in a timely fashion."

  • Subscribe to TCBB in 2014. Click for more information. (PDF)

Editorials


Guest Editorials


Call for Papers


Reviewers List


Access All Recently Published TCBB Articles

RSS Subscribe to the RSS feed of latest TCBB content added to the digital library

Mail Sign up for the Transactions Connection newsletter.


TCBB is a joint publication of the IEEE Computer Society, Association for Computing Machinery, IEEE Computational Intelligence Society, and the IEEE Engineering in Medicine and Biology Society.

IEEE Computer Society    ACM    Computational Intelligence Society    Engineering in Medicine and Biology Society

Published in cooperation with: IEEE Control Systems Society


MEDLINE      PubMed

Indexed in MEDLINE®/PubMed® & ISI