FRAGTE2: An Enhanced Algorithm to Pre-Select Closely Related Genomes for Bacterial Species Demarcation
We previously reported on FRAGTE (hereafter termed FRAGTE1), a promising algorithm for sieving (pre-selecting genome pairs for whole-genome species demarcation). However, the overall amount of pairs sieved by FRAGTE1 is still large, requiring seriously unaffordable computing cost, especially for lar...
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| Format: | Article |
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Frontiers Media S.A.
2022-05-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.847439/full |
| _version_ | 1811251341919518720 |
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| author | Jiaqi Zeng Jiaqi Zeng Yuxiao Wang Ziyao Wu Yizhuang Zhou |
| author_facet | Jiaqi Zeng Jiaqi Zeng Yuxiao Wang Ziyao Wu Yizhuang Zhou |
| author_sort | Jiaqi Zeng |
| collection | DOAJ |
| description | We previously reported on FRAGTE (hereafter termed FRAGTE1), a promising algorithm for sieving (pre-selecting genome pairs for whole-genome species demarcation). However, the overall amount of pairs sieved by FRAGTE1 is still large, requiring seriously unaffordable computing cost, especially for large datasets. Here, we present FRAGTE2. Tests on simulated genomes, real genomes, and metagenome-assembled genomes revealed that (i) FRAGTE2 outstandingly reduces ~50–60.10% of the overall amount of pairs sieved by FRAGTE1, dramatically decreasing the computing cost required for whole-genome species demarcation afterward; (ii) FRAGTE2 shows superior sensitivity than FRAGTE1; (iii) FRAGTE2 shows higher specificity than FRAGTE1; and (iv) FRAGTE2 is faster than or comparable with FRAGTE1. Besides, FRAGTE2 is independent of genome completeness, the same as FRAGTE1. We therefore recommend FRAGTE2 tailored for sieving to facilitate species demarcation in prokaryotes. |
| first_indexed | 2024-04-12T16:18:05Z |
| format | Article |
| id | doaj.art-4c77ef222d854da0898df8b2adb8f1cc |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-12T16:18:05Z |
| publishDate | 2022-05-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj.art-4c77ef222d854da0898df8b2adb8f1cc2022-12-22T03:25:39ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-05-011310.3389/fmicb.2022.847439847439FRAGTE2: An Enhanced Algorithm to Pre-Select Closely Related Genomes for Bacterial Species DemarcationJiaqi Zeng0Jiaqi Zeng1Yuxiao Wang2Ziyao Wu3Yizhuang Zhou4Institute of Pathogeny Biology, School of Basic Medicine, Guilin Medical University, Guilin, ChinaGuangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, School of Public Health, Guilin Medical University, Guilin, ChinaGuangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, School of Public Health, Guilin Medical University, Guilin, ChinaGuangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, School of Public Health, Guilin Medical University, Guilin, ChinaGuangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, School of Public Health, Guilin Medical University, Guilin, ChinaWe previously reported on FRAGTE (hereafter termed FRAGTE1), a promising algorithm for sieving (pre-selecting genome pairs for whole-genome species demarcation). However, the overall amount of pairs sieved by FRAGTE1 is still large, requiring seriously unaffordable computing cost, especially for large datasets. Here, we present FRAGTE2. Tests on simulated genomes, real genomes, and metagenome-assembled genomes revealed that (i) FRAGTE2 outstandingly reduces ~50–60.10% of the overall amount of pairs sieved by FRAGTE1, dramatically decreasing the computing cost required for whole-genome species demarcation afterward; (ii) FRAGTE2 shows superior sensitivity than FRAGTE1; (iii) FRAGTE2 shows higher specificity than FRAGTE1; and (iv) FRAGTE2 is faster than or comparable with FRAGTE1. Besides, FRAGTE2 is independent of genome completeness, the same as FRAGTE1. We therefore recommend FRAGTE2 tailored for sieving to facilitate species demarcation in prokaryotes.https://www.frontiersin.org/articles/10.3389/fmicb.2022.847439/fullspeciesbacterial genomeaverage nucleotide identitytetranucleotidebacterial identificationbioinformatics |
| spellingShingle | Jiaqi Zeng Jiaqi Zeng Yuxiao Wang Ziyao Wu Yizhuang Zhou FRAGTE2: An Enhanced Algorithm to Pre-Select Closely Related Genomes for Bacterial Species Demarcation Frontiers in Microbiology species bacterial genome average nucleotide identity tetranucleotide bacterial identification bioinformatics |
| title | FRAGTE2: An Enhanced Algorithm to Pre-Select Closely Related Genomes for Bacterial Species Demarcation |
| title_full | FRAGTE2: An Enhanced Algorithm to Pre-Select Closely Related Genomes for Bacterial Species Demarcation |
| title_fullStr | FRAGTE2: An Enhanced Algorithm to Pre-Select Closely Related Genomes for Bacterial Species Demarcation |
| title_full_unstemmed | FRAGTE2: An Enhanced Algorithm to Pre-Select Closely Related Genomes for Bacterial Species Demarcation |
| title_short | FRAGTE2: An Enhanced Algorithm to Pre-Select Closely Related Genomes for Bacterial Species Demarcation |
| title_sort | fragte2 an enhanced algorithm to pre select closely related genomes for bacterial species demarcation |
| topic | species bacterial genome average nucleotide identity tetranucleotide bacterial identification bioinformatics |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.847439/full |
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