2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome
Abstract Background Genomic islands are associated with microbial adaptations, carrying genomic signatures different from the host. Some methods perform an overall test to identify genomic islands based on their local features. However, regions of different scales will display different genomic feat...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-04-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-020-3501-2 |
| _version_ | 1819014898333515776 |
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| author | Rui Kong Xinnan Xu Xiaoqing Liu Pingan He Michael Q. Zhang Qi Dai |
| author_facet | Rui Kong Xinnan Xu Xiaoqing Liu Pingan He Michael Q. Zhang Qi Dai |
| author_sort | Rui Kong |
| collection | DOAJ |
| description | Abstract Background Genomic islands are associated with microbial adaptations, carrying genomic signatures different from the host. Some methods perform an overall test to identify genomic islands based on their local features. However, regions of different scales will display different genomic features. Results We proposed here a novel method “2SigFinder “, the first combined use of small-scale and large-scale statistical testing for genomic island detection. The proposed method was tested by genomic island boundary detection and identification of genomic islands or functional features of real biological data. We also compared the proposed method with the comparative genomics and composition-based approaches. The results indicate that the proposed 2SigFinder is more efficient in identifying genomic islands. Conclusions From real biological data, 2SigFinder identified genomic islands from a single genome and reported robust results across different experiments, without annotated information of genomes or prior knowledge from other datasets. 2SigHunter identified 25 Pathogenicity, 1 tRNA, 2 Virulence and 2 Repeats from 27 Pathogenicity, 1 tRNA, 2 Virulence and 2 Repeats, and detected 101 Phage and 28 HEG out of 130 Phage and 36 HEGs in S. enterica Typhi CT18, which shows that it is more efficient in detecting functional features associated with GIs. |
| first_indexed | 2024-12-21T02:23:09Z |
| format | Article |
| id | doaj.art-aa1d54d34425433ab2664213452820a1 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-21T02:23:09Z |
| publishDate | 2020-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-aa1d54d34425433ab2664213452820a12022-12-21T19:19:05ZengBMCBMC Bioinformatics1471-21052020-04-0121111510.1186/s12859-020-3501-22SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genomeRui Kong0Xinnan Xu1Xiaoqing Liu2Pingan He3Michael Q. Zhang4Qi Dai5College of Life Sciences, Zhejiang Sci-Tech UniversityCollege of Life Sciences, Zhejiang Sci-Tech UniversityCollege of Science, Hangzhou Dianzi UniversityCollege of Science, Zhejiang Sci-Tech UniversityDepartment of Biological Sciences, Center for Systems Biology, University of Texas at DallasCollege of Life Sciences, Zhejiang Sci-Tech UniversityAbstract Background Genomic islands are associated with microbial adaptations, carrying genomic signatures different from the host. Some methods perform an overall test to identify genomic islands based on their local features. However, regions of different scales will display different genomic features. Results We proposed here a novel method “2SigFinder “, the first combined use of small-scale and large-scale statistical testing for genomic island detection. The proposed method was tested by genomic island boundary detection and identification of genomic islands or functional features of real biological data. We also compared the proposed method with the comparative genomics and composition-based approaches. The results indicate that the proposed 2SigFinder is more efficient in identifying genomic islands. Conclusions From real biological data, 2SigFinder identified genomic islands from a single genome and reported robust results across different experiments, without annotated information of genomes or prior knowledge from other datasets. 2SigHunter identified 25 Pathogenicity, 1 tRNA, 2 Virulence and 2 Repeats from 27 Pathogenicity, 1 tRNA, 2 Virulence and 2 Repeats, and detected 101 Phage and 28 HEG out of 130 Phage and 36 HEGs in S. enterica Typhi CT18, which shows that it is more efficient in detecting functional features associated with GIs.http://link.springer.com/article/10.1186/s12859-020-3501-2Genomic island detectionGenomic signatureSmall scale testLarge scale testBoundary detection |
| spellingShingle | Rui Kong Xinnan Xu Xiaoqing Liu Pingan He Michael Q. Zhang Qi Dai 2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome BMC Bioinformatics Genomic island detection Genomic signature Small scale test Large scale test Boundary detection |
| title | 2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome |
| title_full | 2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome |
| title_fullStr | 2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome |
| title_full_unstemmed | 2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome |
| title_short | 2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome |
| title_sort | 2sigfinder the combined use of small scale and large scale statistical testing for genomic island detection from a single genome |
| topic | Genomic island detection Genomic signature Small scale test Large scale test Boundary detection |
| url | http://link.springer.com/article/10.1186/s12859-020-3501-2 |
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