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For: Boyce K, Sievers F, Higgins DG. Simple chained guide trees give high-quality protein multiple sequence alignments. Proc Natl Acad Sci U S A 2014;111:10556-61. [PMID: 25002495 DOI: 10.1073/pnas.1405628111] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
Number Cited by Other Article(s)
1
Becker F, Stanke M. learnMSA2: deep protein multiple alignments with large language and hidden Markov models. Bioinformatics 2024;40:ii79-ii86. [PMID: 39230690 PMCID: PMC11373405 DOI: 10.1093/bioinformatics/btae381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]  Open
2
Yeo H, Mehta V, Gulati A, Drew D. Structure and electromechanical coupling of a voltage-gated Na+/H+ exchanger. Nature 2023;623:193-201. [PMID: 37880360 PMCID: PMC10620092 DOI: 10.1038/s41586-023-06518-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/04/2023] [Indexed: 10/27/2023]
3
Yan W, Zhong Y, Hu X, Xu T, Zhang Y, Kales S, Qu Y, Talley DC, Baljinnyam B, LeClair CA, Simeonov A, Polster BM, Huang R, Ye Y, Rai G, Henderson MJ, Tao D, Fang S. Auranofin targets UBA1 and enhances UBA1 activity by facilitating ubiquitin trans-thioesterification to E2 ubiquitin-conjugating enzymes. Nat Commun 2023;14:4798. [PMID: 37558718 PMCID: PMC10412574 DOI: 10.1038/s41467-023-40537-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/25/2023] [Indexed: 08/11/2023]  Open
4
Santus L, Garriga E, Deorowicz S, Gudyś A, Notredame C. Towards the accurate alignment of over a million protein sequences: Current state of the art. Curr Opin Struct Biol 2023;80:102577. [PMID: 37012200 DOI: 10.1016/j.sbi.2023.102577] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 04/04/2023]
5
Zhang Y, Zhang Q, Liu Y, Lin M, Ding C. Multiple Sequence Alignment based on deep Q Network with negative feedback policy. Comput Biol Chem 2022;101:107780. [DOI: 10.1016/j.compbiolchem.2022.107780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/27/2022] [Accepted: 10/18/2022] [Indexed: 11/28/2022]
6
Chao J, Tang F, Xu L. Developments in Algorithms for Sequence Alignment: A Review. Biomolecules 2022;12:biom12040546. [PMID: 35454135 PMCID: PMC9024764 DOI: 10.3390/biom12040546] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 01/27/2023]  Open
7
Maiolo M, Gatti L, Frei D, Leidi T, Gil M, Anisimova M. ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process. BMC Bioinformatics 2021;22:518. [PMID: 34689750 PMCID: PMC8543915 DOI: 10.1186/s12859-021-04442-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 10/13/2021] [Indexed: 11/10/2022]  Open
8
Sievers F, Higgins DG. The Clustal Omega Multiple Alignment Package. Methods Mol Biol 2021;2231:3-16. [PMID: 33289883 DOI: 10.1007/978-1-0716-1036-7_1] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
9
Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform 2020;20:1160-1166. [PMID: 28968734 PMCID: PMC6781576 DOI: 10.1093/bib/bbx108] [Citation(s) in RCA: 4436] [Impact Index Per Article: 887.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/27/2017] [Indexed: 11/28/2022]  Open
10
Nute M, Saleh E, Warnow T. Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets. Syst Biol 2019;68:396-411. [PMID: 30329135 PMCID: PMC6472439 DOI: 10.1093/sysbio/syy068] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 09/27/2018] [Accepted: 10/11/2018] [Indexed: 01/15/2023]  Open
11
Mangul S, Martin LS, Hill BL, Lam AKM, Distler MG, Zelikovsky A, Eskin E, Flint J. Systematic benchmarking of omics computational tools. Nat Commun 2019;10:1393. [PMID: 30918265 PMCID: PMC6437167 DOI: 10.1038/s41467-019-09406-4] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 03/06/2019] [Indexed: 01/11/2023]  Open
12
Chatzou M, Floden EW, Di Tommaso P, Gascuel O, Notredame C. Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty. Syst Biol 2018;67:997-1009. [PMID: 30295908 DOI: 10.1093/sysbio/syx096] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 12/17/2017] [Indexed: 01/01/2023]  Open
13
Maiolo M, Zhang X, Gil M, Anisimova M. Progressive multiple sequence alignment with indel evolution. BMC Bioinformatics 2018;19:331. [PMID: 30241460 PMCID: PMC6151001 DOI: 10.1186/s12859-018-2357-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 09/03/2018] [Indexed: 12/30/2022]  Open
14
Sievers F, Higgins DG. Clustal Omega for making accurate alignments of many protein sequences. Protein Sci 2017;27:135-145. [PMID: 28884485 DOI: 10.1002/pro.3290] [Citation(s) in RCA: 1207] [Impact Index Per Article: 150.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/01/2017] [Accepted: 09/05/2017] [Indexed: 01/05/2023]
15
Akand EH, Downard KM. Mutational analysis employing a phylogenetic mass tree approach in a study of the evolution of the influenza virus. Mol Phylogenet Evol 2017;112:209-217. [DOI: 10.1016/j.ympev.2017.04.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 03/29/2017] [Accepted: 04/05/2017] [Indexed: 11/28/2022]
16
Baichoo S, Ouzounis CA. Computational complexity of algorithms for sequence comparison, short-read assembly and genome alignment. Biosystems 2017;156-157:72-85. [PMID: 28392341 DOI: 10.1016/j.biosystems.2017.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 12/12/2022]
17
Gudyś A, Deorowicz S. QuickProbs 2: Towards rapid construction of high-quality alignments of large protein families. Sci Rep 2017;7:41553. [PMID: 28139687 PMCID: PMC5282490 DOI: 10.1038/srep41553] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/21/2016] [Indexed: 01/05/2023]  Open
18
Deorowicz S, Debudaj-Grabysz A, Gudyś A. FAMSA: Fast and accurate multiple sequence alignment of huge protein families. Sci Rep 2016;6:33964. [PMID: 27670777 PMCID: PMC5037421 DOI: 10.1038/srep33964] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/31/2016] [Indexed: 11/10/2022]  Open
19
Yamada KD, Tomii K, Katoh K. Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees. Bioinformatics 2016;32:3246-3251. [PMID: 27378296 PMCID: PMC5079479 DOI: 10.1093/bioinformatics/btw412] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/20/2016] [Indexed: 11/26/2022]  Open
20
Neuwald AF, Altschul SF. Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties. PLoS Comput Biol 2016;12:e1004936. [PMID: 27192614 PMCID: PMC4871425 DOI: 10.1371/journal.pcbi.1004936] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 04/24/2016] [Indexed: 11/19/2022]  Open
21
Fox G, Sievers F, Higgins DG. Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments. ACTA ACUST UNITED AC 2015;32:814-20. [PMID: 26568625 PMCID: PMC5939968 DOI: 10.1093/bioinformatics/btv592] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 10/10/2015] [Indexed: 01/03/2023]
22
Boyce K, Sievers F, Higgins DG. Instability in progressive multiple sequence alignment algorithms. Algorithms Mol Biol 2015;10:26. [PMID: 26457114 PMCID: PMC4599319 DOI: 10.1186/s13015-015-0057-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/29/2015] [Indexed: 11/10/2022]  Open
23
Wright ES. DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. BMC Bioinformatics 2015;16:322. [PMID: 26445311 PMCID: PMC4595117 DOI: 10.1186/s12859-015-0749-z] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/23/2015] [Indexed: 12/20/2022]  Open
24
Reply to Tan et al.: Differences between real and simulated proteins in multiple sequence alignments. Proc Natl Acad Sci U S A 2015;112:E101. [PMID: 25564671 DOI: 10.1073/pnas.1419351112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
25
Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks. Proc Natl Acad Sci U S A 2015;112:E99-100. [PMID: 25564672 DOI: 10.1073/pnas.1417526112] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
26
Sievers F, Higgins DG. Clustal omega. ACTA ACUST UNITED AC 2014;48:3.13.1-3.13.16. [PMID: 25501942 DOI: 10.1002/0471250953.bi0313s48] [Citation(s) in RCA: 438] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
27
Systematic exploration of guide-tree topology effects for small protein alignments. BMC Bioinformatics 2014;15:338. [PMID: 25282640 PMCID: PMC4287568 DOI: 10.1186/1471-2105-15-338] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/25/2014] [Indexed: 11/21/2022]  Open
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