title: QuickProbs 2: Towards rapid construction of high-quality alignments of large protein families.
abstract: The ever-increasing size of sequence databases caused by the development of high throughput sequencing, poses to multiple alignment algorithms one of the greatest challenges yet. As we show, well-established techniques employed for increasing alignment quality, i.e., refinement and consistency, are ineffective when large protein families are investigated. We present QuickProbs 2, an algorithm for multiple sequence alignment. Based on probabilistic models, equipped with novel column-oriented refinement and selective consistency, it offers outstanding accuracy. When analysing hundreds of sequences, Quick-Probs 2 is noticeably better than ClustalΩ and MAFFT, the previous leaders for processing numerous protein families. In the case of smaller sets, for which consistency-based methods are the best performing, QuickProbs 2 is also superior to the competitors. Due to low computational requirements of selective consistency and utilization of massively parallel architectures, presented algorithm has similar execution times to ClustalΩ, and is orders of magnitude faster than full consistency approaches, like MSAProbs or PicXAA. All these make QuickProbs 2 an excellent tool for aligning families ranging from few, to hundreds of proteins.
authors.affiliation: Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland.
authors.forename: Adam
authors.initials: A
authors.lastname: Gudyś
authors.affiliation: Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Deorowicz
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D011506:Proteins