Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics [version 1; referees: 1 approved, 2 approved with reservations]
A functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. Detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for simi...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2016-08-01
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| Series: | F1000Research |
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| Online Access: | http://f1000research.com/articles/5-1987/v1 |
| _version_ | 1828894405097947136 |
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| author | Jasper J. Koehorst Edoardo Saccenti Peter J. Schaap Vitor A. P. Martins dos Santos Maria Suarez-Diez |
| author_facet | Jasper J. Koehorst Edoardo Saccenti Peter J. Schaap Vitor A. P. Martins dos Santos Maria Suarez-Diez |
| author_sort | Jasper J. Koehorst |
| collection | DOAJ |
| description | A functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. Detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. We investigated the use of protein domain architectures for large scale functional comparative analysis as an alternative method. The performance of both approaches was assessed through functional comparison of 446 bacterial genomes sampled at different taxonomic levels. We show that protein domain architectures provide a fast and efficient alternative to methods based on sequence similarity to identify groups of functionally equivalent proteins within and across taxonomic bounderies. As the computational cost scales linearly, and not quadratically with the number of genomes, it is suitable for large scale comparative analysis. Running both methods in parallel pinpoints potential functional adaptations that may add to bacterial fitness. |
| first_indexed | 2024-12-13T14:09:59Z |
| format | Article |
| id | doaj.art-22dc75771d6846f5a1f3de6b3c6f88a9 |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-12-13T14:09:59Z |
| publishDate | 2016-08-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-22dc75771d6846f5a1f3de6b3c6f88a92022-12-21T23:42:29ZengF1000 Research LtdF1000Research2046-14022016-08-01510.12688/f1000research.9416.110140Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics [version 1; referees: 1 approved, 2 approved with reservations]Jasper J. Koehorst0Edoardo Saccenti1Peter J. Schaap2Vitor A. P. Martins dos Santos3Maria Suarez-Diez4Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng, NetherlandsLaboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng, NetherlandsLaboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng, NetherlandsLifeGlimmer, GmBH, Berlin, GermanyLaboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng, NetherlandsA functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. Detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. We investigated the use of protein domain architectures for large scale functional comparative analysis as an alternative method. The performance of both approaches was assessed through functional comparison of 446 bacterial genomes sampled at different taxonomic levels. We show that protein domain architectures provide a fast and efficient alternative to methods based on sequence similarity to identify groups of functionally equivalent proteins within and across taxonomic bounderies. As the computational cost scales linearly, and not quadratically with the number of genomes, it is suitable for large scale comparative analysis. Running both methods in parallel pinpoints potential functional adaptations that may add to bacterial fitness.http://f1000research.com/articles/5-1987/v1GenomicsMicrobial Evolution & Genomics |
| spellingShingle | Jasper J. Koehorst Edoardo Saccenti Peter J. Schaap Vitor A. P. Martins dos Santos Maria Suarez-Diez Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics [version 1; referees: 1 approved, 2 approved with reservations] F1000Research Genomics Microbial Evolution & Genomics |
| title | Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics [version 1; referees: 1 approved, 2 approved with reservations] |
| title_full | Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics [version 1; referees: 1 approved, 2 approved with reservations] |
| title_fullStr | Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics [version 1; referees: 1 approved, 2 approved with reservations] |
| title_full_unstemmed | Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics [version 1; referees: 1 approved, 2 approved with reservations] |
| title_short | Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics [version 1; referees: 1 approved, 2 approved with reservations] |
| title_sort | protein domain architectures provide a fast efficient and scalable alternative to sequence based methods for comparative functional genomics version 1 referees 1 approved 2 approved with reservations |
| topic | Genomics Microbial Evolution & Genomics |
| url | http://f1000research.com/articles/5-1987/v1 |
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