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For: Naznooshsadat E, Elham P, Ali SZ. FAME: fast and memory efficient multiple sequences alignment tool through compatible chain of roots. Bioinformatics 2020;36:3662-3668. [PMID: 32170927 DOI: 10.1093/bioinformatics/btaa175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/10/2020] [Accepted: 03/12/2020] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Chen YA, Ng PY, Garcia-Ruiz D, Elliot A, Palmer B, Assunção Carvalho RMCD, Tseng LF, Lee CS, Tsai KH, Greenhouse B, Chang HH. Genetic surveillance reveals low but sustained malaria transmission with clonal replacement in Sao Tome and Principe. COMMUNICATIONS MEDICINE 2025;5:199. [PMID: 40425726 PMCID: PMC12116912 DOI: 10.1038/s43856-025-00905-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Accepted: 05/09/2025] [Indexed: 05/29/2025]  Open
2
Chen Y, Ng PY, Garcia D, Elliot A, Palmer B, Assunção Carvalho RMCD, Tseng LF, Lee CS, Tsai KH, Greenhouse B, Chang HH. Genetic surveillance reveals low, sustained malaria transmission with clonal replacement in Sao Tome and Principe. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.15.24309968. [PMID: 39072035 PMCID: PMC11275696 DOI: 10.1101/2024.07.15.24309968] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
3
Zhang P, Liu H, Wei Y, Zhai Y, Tian Q, Zou Q. FMAlign2: a novel fast multiple nucleotide sequence alignment method for ultralong datasets. Bioinformatics 2024;40:btae014. [PMID: 38200554 PMCID: PMC10809904 DOI: 10.1093/bioinformatics/btae014] [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] [Received: 07/29/2023] [Revised: 12/27/2023] [Accepted: 01/09/2024] [Indexed: 01/12/2024]  Open
4
Zheng H, Marçais G, Kingsford C. Creating and Using Minimizer Sketches in Computational Genomics. J Comput Biol 2023;30:1251-1276. [PMID: 37646787 PMCID: PMC11082048 DOI: 10.1089/cmb.2023.0094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]  Open
5
Wei Y, Zou Q, Tang F, Yu L. WMSA: a novel method for multiple sequence alignment of DNA sequences. Bioinformatics 2022;38:5019-5025. [PMID: 36179076 DOI: 10.1093/bioinformatics/btac658] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/30/2022] [Accepted: 09/29/2022] [Indexed: 12/24/2022]  Open
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
Zhang Y, Zhang Q, Zhou J, Zou Q. A survey on the algorithm and development of multiple sequence alignment. Brief Bioinform 2022;23:6546258. [PMID: 35272347 DOI: 10.1093/bib/bbac069] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/30/2022] [Accepted: 02/09/2022] [Indexed: 12/21/2022]  Open
8
Biological sequence analysis. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00003-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
9
Liu H, Zou Q, Xu Y. A novel fast multiple nucleotide sequence alignment method based on FM-index. Brief Bioinform 2021;23:6458932. [PMID: 34893794 DOI: 10.1093/bib/bbab519] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/19/2021] [Accepted: 11/14/2021] [Indexed: 11/13/2022]  Open
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