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For: 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] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 10/10/2015] [Indexed: 01/03/2023]
Number Cited by Other Article(s)
1
Shrestha B, Adhikari B. Scoring protein sequence alignments using deep Learning. Bioinformatics 2022;38:2988-2995. [PMID: 35385080 DOI: 10.1093/bioinformatics/btac210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 11/12/2022]  Open
2
Lladós J, Cores F, Guirado F, Lérida JL. Accurate consistency-based MSA reducing the memory footprint. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2021;208:106237. [PMID: 34198017 DOI: 10.1016/j.cmpb.2021.106237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
3
Wright ES. RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency. RNA (NEW YORK, N.Y.) 2020;26:531-540. [PMID: 32005745 PMCID: PMC7161358 DOI: 10.1261/rna.073015.119] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/28/2020] [Indexed: 05/05/2023]
4
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
5
Torrisi M, Pollastri G, Le Q. Deep learning methods in protein structure prediction. Comput Struct Biotechnol J 2020;18:1301-1310. [PMID: 32612753 PMCID: PMC7305407 DOI: 10.1016/j.csbj.2019.12.011] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 01/01/2023]  Open
6
Fukuda H, Tomii K. DeepECA: an end-to-end learning framework for protein contact prediction from a multiple sequence alignment. BMC Bioinformatics 2020;21:10. [PMID: 31918654 PMCID: PMC6953294 DOI: 10.1186/s12859-019-3190-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/04/2019] [Indexed: 12/30/2022]  Open
7
Modi V, Dunbrack RL. A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains. Sci Rep 2019;9:19790. [PMID: 31875044 PMCID: PMC6930252 DOI: 10.1038/s41598-019-56499-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/14/2019] [Indexed: 12/21/2022]  Open
8
Nakamura T, Yamada KD, Tomii K, Katoh K. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics 2019;34:2490-2492. [PMID: 29506019 PMCID: PMC6041967 DOI: 10.1093/bioinformatics/bty121] [Citation(s) in RCA: 612] [Impact Index Per Article: 102.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/28/2018] [Indexed: 12/03/2022]  Open
9
Sievers F, Higgins DG. QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction. Bioinformatics 2019;36:90-95. [PMID: 31292629 PMCID: PMC9881607 DOI: 10.1093/bioinformatics/btz552] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/17/2019] [Accepted: 07/09/2019] [Indexed: 02/02/2023]  Open
10
Le Q, Sievers F, Higgins DG. Protein multiple sequence alignment benchmarking through secondary structure prediction. Bioinformatics 2018;33:1331-1337. [PMID: 28093407 PMCID: PMC5408826 DOI: 10.1093/bioinformatics/btw840] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/10/2017] [Indexed: 12/26/2022]  Open
11
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]
12
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
13
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
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