SUMMARY: Partial order alignment, which aligns a sequence to a directed acyclic graph, is now frequently used as a key component in long-read error correction and assembly. We present abPOA (adaptive banded Partial Order Alignment), a Single Instruction Multiple Data (SIMD)-based C library for fast partial order alignment using adaptive banded dynamic programming. It can work as a stand-alone multiple sequence alignment and consensus calling tool or be easily integrated into any long-read error correction and assembly workflow. Compared to a state-of-the-art tool (SPOA), abPOA is up to 10 times faster with a comparable alignment accuracy. AVAILABILITY AND IMPLEMENTATION: abPOA is implemented in C. A stand-alone tool and a C/Python software interface are freely available at https://github.com/yangao07/abPOA. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Bioinformatics, 2021, 37(15), 2209–2211. doi: https://doi.org/10.1093/bioinformatics/btaa963 Upon the original publication of this article, the affiliation: “Center for Bioinformatics, Department of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China” was inadvertently omitted prior to publication. The affiliation has been reinstated.

Although there exist numerous literatures on facility layout in manufacturing systems, studies on department layout in hospitals are relatively scarce. In this paper, we proposed a MOEA/D based approach for a hospital department layout problem, where three objectives are simultaneously optimized, namely patient flow cost, the closeness of departments and rearrangement cost. A constraint handling technology is introduced to deal with infeasible solutions. Experiments show that the proposed approach is able to get satisfactory Pareto solutions with lower patients' flow cost and the closeness compared to the original layout, and that the optimized layouts decrease the patients' move time, thereby improving quality of service.