Selection of organisms for the co-evolution-based study of protein interactions
<p>Abstract</p> <p>Background</p> <p>The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the <it>mirrortree </it>and related methodologies, is being widely used. Although dep...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2011-09-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/12/363 |
| _version_ | 1818484624120086528 |
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| author | Valencia Alfonso Lopez Daniel Juan David Ochoa David Herman Dorota Pazos Florencio |
| author_facet | Valencia Alfonso Lopez Daniel Juan David Ochoa David Herman Dorota Pazos Florencio |
| author_sort | Valencia Alfonso |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the <it>mirrortree </it>and related methodologies, is being widely used. Although dependence between the performance of these methods and the set of organisms used to build the trees was suspected, so far nobody assessed it in an exhaustive way, and, in general, previous works used as many organisms as possible. In this work we asses the effect of using different sets of organism (chosen according with various phylogenetic criteria) on the performance of this methodology in detecting protein interactions of different nature.</p> <p>Results</p> <p>We show that the performance of three <it>mirrortree</it>-related methodologies depends on the set of organisms used for building the trees, and it is not always directly related to the number of organisms in a simple way. Certain subsets of organisms seem to be more suitable for the predictions of certain types of interactions. This relationship between type of interaction and optimal set of organism for detecting them makes sense in the light of the phylogenetic distribution of the organisms and the nature of the interactions.</p> <p>Conclusions</p> <p>In order to obtain an optimal performance when predicting protein interactions, it is recommended to use different sets of organisms depending on the available computational resources and data, as well as the type of interactions of interest.</p> |
| first_indexed | 2024-12-10T15:57:38Z |
| format | Article |
| id | doaj.art-ecd5a1283c774d8d95e6169c8e52761b |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-10T15:57:38Z |
| publishDate | 2011-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-ecd5a1283c774d8d95e6169c8e52761b2022-12-22T01:42:34ZengBMCBMC Bioinformatics1471-21052011-09-0112136310.1186/1471-2105-12-363Selection of organisms for the co-evolution-based study of protein interactionsValencia AlfonsoLopez DanielJuan DavidOchoa DavidHerman DorotaPazos Florencio<p>Abstract</p> <p>Background</p> <p>The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the <it>mirrortree </it>and related methodologies, is being widely used. Although dependence between the performance of these methods and the set of organisms used to build the trees was suspected, so far nobody assessed it in an exhaustive way, and, in general, previous works used as many organisms as possible. In this work we asses the effect of using different sets of organism (chosen according with various phylogenetic criteria) on the performance of this methodology in detecting protein interactions of different nature.</p> <p>Results</p> <p>We show that the performance of three <it>mirrortree</it>-related methodologies depends on the set of organisms used for building the trees, and it is not always directly related to the number of organisms in a simple way. Certain subsets of organisms seem to be more suitable for the predictions of certain types of interactions. This relationship between type of interaction and optimal set of organism for detecting them makes sense in the light of the phylogenetic distribution of the organisms and the nature of the interactions.</p> <p>Conclusions</p> <p>In order to obtain an optimal performance when predicting protein interactions, it is recommended to use different sets of organisms depending on the available computational resources and data, as well as the type of interactions of interest.</p>http://www.biomedcentral.com/1471-2105/12/363 |
| spellingShingle | Valencia Alfonso Lopez Daniel Juan David Ochoa David Herman Dorota Pazos Florencio Selection of organisms for the co-evolution-based study of protein interactions BMC Bioinformatics |
| title | Selection of organisms for the co-evolution-based study of protein interactions |
| title_full | Selection of organisms for the co-evolution-based study of protein interactions |
| title_fullStr | Selection of organisms for the co-evolution-based study of protein interactions |
| title_full_unstemmed | Selection of organisms for the co-evolution-based study of protein interactions |
| title_short | Selection of organisms for the co-evolution-based study of protein interactions |
| title_sort | selection of organisms for the co evolution based study of protein interactions |
| url | http://www.biomedcentral.com/1471-2105/12/363 |
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