MOTIVATION: Multiple sequence alignment is of central importance to bioinformatics and computational biology. Although a large number of algorithms for computing a multiple sequence alignment have been designed, the efficient computation of highly accurate multiple alignments is still a challenge. RESULTS: We present MSAProbs, a new and practical multiple alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Furthermore, two critical bioinformatics techniques, namely weighted probabilistic consistency transformation and weighted profile-profile alignment, are incorporated to improve alignment accuracy. Assessed using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. Furthermore, MSAProbs is optimized for multi-core CPUs by employing a multi-threaded design, leading to a competitive execution time compared to other aligners. AVAILABILITY: The source code of MSAProbs, written in C++, is freely and publicly available from http://msaprobs.sourceforge.net.
MOTIVATION: Multiple sequence alignment is of central importance to bioinformatics and computational biology. Although a large number of algorithms for computing a multiple sequence alignment have been designed, the efficient computation of highly accurate multiple alignments is still a challenge. RESULTS: We present MSAProbs, a new and practical multiple alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Furthermore, two critical bioinformatics techniques, namely weighted probabilistic consistency transformation and weighted profile-profile alignment, are incorporated to improve alignment accuracy. Assessed using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. Furthermore, MSAProbs is optimized for multi-core CPUs by employing a multi-threaded design, leading to a competitive execution time compared to other aligners. AVAILABILITY: The source code of MSAProbs, written in C++, is freely and publicly available from http://msaprobs.sourceforge.net.
Authors: Suzanne E McGaugh; Anne M Bronikowski; Chih-Horng Kuo; Dawn M Reding; Elizabeth A Addis; Lex E Flagel; Fredric J Janzen; Tonia S Schwartz Journal: Proc Natl Acad Sci U S A Date: 2015-05-19 Impact factor: 11.205
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Authors: Ayesha Imtiaz; Inna A Belyantseva; Alisha J Beirl; Cristina Fenollar-Ferrer; Rasheeda Bashir; Ihtisham Bukhari; Amal Bouzid; Uzma Shaukat; Hela Azaiez; Kevin T Booth; Kimia Kahrizi; Hossein Najmabadi; Azra Maqsood; Elizabeth A Wilson; Tracy S Fitzgerald; Abdelaziz Tlili; Rafal Olszewski; Merete Lund; Taimur Chaudhry; Atteeq U Rehman; Matthew F Starost; Ali M Waryah; Michael Hoa; Lijin Dong; Robert J Morell; Richard J H Smith; Sheikh Riazuddin; Saber Masmoudi; Katie S Kindt; Sadaf Naz; Thomas B Friedman Journal: Hum Mol Genet Date: 2018-03-01 Impact factor: 6.150
Authors: Lucas C Wheeler; Jeremy A Anderson; Anneliese J Morrison; Caitlyn E Wong; Michael J Harms Journal: Biochemistry Date: 2017-12-29 Impact factor: 3.162