ProbPFP: A Multiple Sequence Alignment Algorithm Combining Partition Function and Hidden Markov Model with Particle Swarm Optimization
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Yadong Wang | Nan Wang | Shuilin Jin | Qinghua Jiang | Qing Zhan | Renjie Tan | Yadong Wang | Nan Wang | Qinghua Jiang | Shuilin Jin | Renjie Tan | Qing Zhan
[1] Yongchao Liu,et al. MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities , 2010, Bioinform..
[2] Cédric Notredame,et al. Multiple sequence alignment modeling: methods and applications , 2016, Briefings Bioinform..
[3] Serafim Batzoglou,et al. CONTRAlign: Discriminative Training for Protein Sequence Alignment , 2006, RECOMB.
[4] Sean R. Eddy,et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .
[5] Thomas Kiel Rasmussen,et al. Improved Hidden Markov Model training for multiple sequence alignment by a particle swarm optimization-evolutionary algorithm hybrid. , 2003, Bio Systems.
[6] Siu-Ming Yiu,et al. GLProbs: aligning multiple sequences adaptively , 2015, TCBB.
[7] Patrice Koehl,et al. MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences , 2005, Nucleic acids research.
[8] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[9] M. Nei,et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.
[10] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[11] Chuong B. Do,et al. ProbCons: Probabilistic consistency-based multiple sequence alignment. , 2005, Genome research.
[12] Xingji Li,et al. Defect evolution in ZnO and its effect on radiation tolerance. , 2018, Physical chemistry chemical physics : PCCP.
[13] Xingji Li,et al. Bright room temperature single photon source at telecom range in cubic silicon carbide , 2018, Nature Communications.
[14] Moon-Jung Chung,et al. Multiple sequence alignment using simulated annealing , 1994, Comput. Appl. Biosci..
[15] Olivier Poch,et al. GOAnno: GO annotation based on multiple alignment , 2005, Bioinform..
[16] Xiaojun Wu,et al. Multiple Sequence Alignment with Hidden Markov Models Learned by Random Drift Particle Swarm Optimization , 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[17] Jie Sun,et al. DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function , 2018, Bioinform..
[18] Jiajie Peng,et al. InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk , 2018, BMC Genomics.
[19] D. Higgins,et al. T-Coffee: A novel method for fast and accurate multiple sequence alignment. , 2000, Journal of molecular biology.
[20] Wanying Xu,et al. OAHG: an integrated resource for annotating human genes with multi-level ontologies , 2016, Scientific Reports.
[21] D. Haussler,et al. Hidden Markov models in computational biology. Applications to protein modeling. , 1993, Journal of molecular biology.
[22] Yadong Wang,et al. Identifying term relations cross different gene ontology categories , 2017, BMC Bioinformatics.
[23] Meng Zhou,et al. MetSigDis: a manually curated resource for the metabolic signatures of diseases , 2019, Briefings Bioinform..
[24] Yue Jiang,et al. DisSim: an online system for exploring significant similar diseases and exhibiting potential therapeutic drugs , 2016, Scientific Reports.
[25] Jiajie Peng,et al. Measuring phenotype-phenotype similarity through the interactome , 2017, BIBM.
[26] Byung-Jun Yoon,et al. PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences , 2010, Nucleic acids research.
[27] Xiaojun Wu,et al. Multiple sequence alignment using the Hidden Markov Model trained by an improved quantum-behaved particle swarm optimization , 2012, Inf. Sci..
[28] Burkhard Morgenstern,et al. DIALIGN at GOBICS—multiple sequence alignment using various sources of external information , 2013, Nucleic Acids Res..
[29] Yadong Wang,et al. A novel method to measure the semantic similarity of HPO terms , 2017, Int. J. Data Min. Bioinform..
[30] Qinghua Guo,et al. LncRNA2Target v2.0: a comprehensive database for target genes of lncRNAs in human and mouse , 2018, Nucleic Acids Res..
[31] Olivier Poch,et al. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs , 1999, Bioinform..
[32] Lode Wyns,et al. Align-m-a new algorithm for multiple alignment of highly divergent sequences , 2004, Bioinform..
[33] Riccardo Poli,et al. Particle swarm optimization , 1995, Swarm Intelligence.
[34] Yu Zhang,et al. Multiple Sequence Alignment Based on Profile Hidden Markov Model and Quantum-Behaved Particle Swarm Optimization with Selection Method , 2011 .
[35] D. Higgins,et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.
[36] Liang Cheng,et al. Measuring disease similarity and predicting disease-related ncRNAs by a novel method , 2017, BMC Medical Genomics.
[37] E. Sonnhammer,et al. Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features , 2008, Nucleic acids research.
[38] Richa Agarwala,et al. COBALT: constraint-based alignment tool for multiple protein sequences , 2007, Bioinform..
[39] Jun Zhang,et al. Identifying diseases-related metabolites using random walk , 2018, BMC Bioinformatics.
[40] Liang Cheng,et al. Rs4878104 contributes to Alzheimer’s disease risk and regulates DAPK1 gene expression , 2017, Neurological Sciences.
[41] M. Ruggero,et al. Similarity of Traveling-Wave Delays in the Hearing Organs of Humans and Other Tetrapods , 2007, Journal for the Association for Research in Otolaryngology.
[42] Dennis R. Livesay,et al. Probalign: multiple sequence alignment using partition function posterior probabilities , 2006, Bioinform..
[43] Shuhui Liu,et al. Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach , 2018, BMC Systems Biology.
[44] Gajendra P. S. Raghava,et al. OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy , 2003, BMC Bioinformatics.
[45] K. Katoh,et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.
[46] Liang Cheng,et al. GAB2 rs2373115 variant contributes to Alzheimer's disease risk specifically in European population , 2017, Journal of the Neurological Sciences.