1. Pin-Align: A New Dynamic Programming Approach to Align Protein-Protein Interaction Networks
- Author
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Farid Amir-Ghiasvand, Vida Momenzadeh, and Abbas Nowzari-Dalini
- Subjects
Article Subject ,Computer science ,Sequence alignment ,computer.software_genre ,Machine learning ,lcsh:Computer applications to medicine. Medical informatics ,General Biochemistry, Genetics and Molecular Biology ,Mice ,Software ,Protein Interaction Mapping ,Animals ,Cluster Analysis ,Humans ,Sensitivity (control systems) ,Protein Interaction Maps ,KEGG ,Databases, Protein ,Network model ,Probability ,Smith–Waterman algorithm ,General Immunology and Microbiology ,business.industry ,Applied Mathematics ,Computational Biology ,Proteins ,Reproducibility of Results ,General Medicine ,Dynamic programming ,Modeling and Simulation ,Scalability ,lcsh:R858-859.7 ,Artificial intelligence ,Data mining ,business ,computer ,Sequence Alignment ,Algorithms ,Research Article - Abstract
To date, few tools for aligning protein-protein interaction networks have been suggested. These tools typically find conserved interaction patterns using various local or global alignment algorithms. However, the improvement of the speed, scalability, simplification, and accuracy of network alignment tools is still the target of new researches. In this paper, we introducePin-Align, a new tool for local alignment of protein-protein interaction networks.Pin-Alignaccuracy is tested on protein interaction networks from IntAct, DIP, and the Stanford Network Database and the results are compared with other well-known algorithms. It is shown thatPin-Alignhas higher sensitivity and specificity in terms of KEGG Ortholog groups.
- Published
- 2014