LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis
Distinct bacteria are able to cope with highly diverse lifestyles; for instance, they can be free living or host-associated. Thus, these organisms must possess a large and varied genomic arsenal to withstand different environmental conditions. To facilitate the identification of genomic features tha...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
De Gruyter
2017-07-01
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| Series: | Journal of Integrative Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1515/jib-2017-0010 |
| _version_ | 1818733587794493440 |
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| author | Barbosa Eudes Röttger Richard Hauschild Anne-Christin de Castro Soares Siomar Böcker Sebastian Azevedo Vasco Baumbach Jan |
| author_facet | Barbosa Eudes Röttger Richard Hauschild Anne-Christin de Castro Soares Siomar Böcker Sebastian Azevedo Vasco Baumbach Jan |
| author_sort | Barbosa Eudes |
| collection | DOAJ |
| description | Distinct bacteria are able to cope with highly diverse lifestyles; for instance, they can be free living or host-associated. Thus, these organisms must possess a large and varied genomic arsenal to withstand different environmental conditions. To facilitate the identification of genomic features that might influence bacterial adaptation to a specific niche, we introduce LifeStyle-Specific-Islands (LiSSI). LiSSI combines evolutionary sequence analysis with statistical learning (Random Forest with feature selection, model tuning and robustness analysis). In summary, our strategy aims to identify conserved consecutive homology sequences (islands) in genomes and to identify the most discriminant islands for each lifestyle. |
| first_indexed | 2024-12-17T23:51:51Z |
| format | Article |
| id | doaj.art-3b1e2c33bcd7496a925afaa042134663 |
| institution | Directory Open Access Journal |
| issn | 1613-4516 |
| language | English |
| last_indexed | 2024-12-17T23:51:51Z |
| publishDate | 2017-07-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Journal of Integrative Bioinformatics |
| spelling | doaj.art-3b1e2c33bcd7496a925afaa0421346632022-12-21T21:28:11ZengDe GruyterJournal of Integrative Bioinformatics1613-45162017-07-011421366137210.1515/jib-2017-0010jib-2017-0010LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island AnalysisBarbosa Eudes0Röttger Richard1Hauschild Anne-Christin2de Castro Soares Siomar3Böcker Sebastian4Azevedo Vasco5Baumbach Jan6University of Southern Denmark, Department of Mathematics and Computer Science, Odense, DenmarkUniversity of Southern Denmark, Department of Mathematics and Computer Science, Odense, DenmarkUniversity of Southern Denmark, Department of Mathematics and Computer Science, Odense, DenmarkFederal University of Minas Gerais, Institute of Biological Sciences, Belo Horizonte, BrazilFriedrich-Schiller-Universität Jena, Faculty of Mathematics and Computer Science, Jena, GermanyFederal University of Minas Gerais, Institute of Biological Sciences, Belo Horizonte, BrazilUniversity of Southern Denmark, Department of Mathematics and Computer Science, Odense, DenmarkDistinct bacteria are able to cope with highly diverse lifestyles; for instance, they can be free living or host-associated. Thus, these organisms must possess a large and varied genomic arsenal to withstand different environmental conditions. To facilitate the identification of genomic features that might influence bacterial adaptation to a specific niche, we introduce LifeStyle-Specific-Islands (LiSSI). LiSSI combines evolutionary sequence analysis with statistical learning (Random Forest with feature selection, model tuning and robustness analysis). In summary, our strategy aims to identify conserved consecutive homology sequences (islands) in genomes and to identify the most discriminant islands for each lifestyle.https://doi.org/10.1515/jib-2017-0010bacterialifestylemachine learningislandhomologous genes |
| spellingShingle | Barbosa Eudes Röttger Richard Hauschild Anne-Christin de Castro Soares Siomar Böcker Sebastian Azevedo Vasco Baumbach Jan LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis Journal of Integrative Bioinformatics bacteria lifestyle machine learning island homologous genes |
| title | LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis |
| title_full | LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis |
| title_fullStr | LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis |
| title_full_unstemmed | LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis |
| title_short | LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis |
| title_sort | lifestyle specific islands lissi integrated bioinformatics platform for genomic island analysis |
| topic | bacteria lifestyle machine learning island homologous genes |
| url | https://doi.org/10.1515/jib-2017-0010 |
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