Exploration of phylogenetic data using a global sequence analysis method
<p>Abstract</p> <p>Background</p> <p>Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2005-11-01
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| Series: | BMC Evolutionary Biology |
| Online Access: | http://www.biomedcentral.com/1471-2148/5/63 |
| _version_ | 1818978896985456640 |
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| author | Giron Alain Edwards Scott Dufraigne Christine Chapus Charles Fertil Bernard Deschavanne Patrick |
| author_facet | Giron Alain Edwards Scott Dufraigne Christine Chapus Charles Fertil Bernard Deschavanne Patrick |
| author_sort | Giron Alain |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets.</p> <p>Results</p> <p>Here we explore the phylogenetic signal present in molecular data by genomic signatures, defined as the set of frequencies of short oligonucleotides present in DNA sequences. Although violating many of the standard assumptions of traditional phylogenetic analyses – in particular explicit statements of homology inherent in character matrices – the use of the signature does permit the analysis of very long sequences, even those that are unalignable, and is therefore most useful in cases where alignment is questionable. We compare the results obtained by traditional phylogenetic methods to those inferred by the signature method for two genes: RAG1, which is easily alignable, and 18S RNA, where alignments are often ambiguous for some regions. We also apply this method to a multigene data set of 33 genes for 9 bacteria and one archea species as well as to the whole genome of a set of 16 γ-proteobacteria. In addition to delivering phylogenetic results comparable to traditional methods, the comparison of signatures for the sequences involved in the bacterial example identified putative candidates for horizontal gene transfers.</p> <p>Conclusion</p> <p>The signature method is therefore a fast tool for exploring phylogenetic data, providing not only a pretreatment for discovering new sequence relationships, but also for identifying cases of sequence evolution that could confound traditional phylogenetic analysis.</p> |
| first_indexed | 2024-12-20T16:50:56Z |
| format | Article |
| id | doaj.art-5b40312cc7214342a044bef7fb00a6b2 |
| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-12-20T16:50:56Z |
| publishDate | 2005-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Evolutionary Biology |
| spelling | doaj.art-5b40312cc7214342a044bef7fb00a6b22022-12-21T19:32:49ZengBMCBMC Evolutionary Biology1471-21482005-11-01516310.1186/1471-2148-5-63Exploration of phylogenetic data using a global sequence analysis methodGiron AlainEdwards ScottDufraigne ChristineChapus CharlesFertil BernardDeschavanne Patrick<p>Abstract</p> <p>Background</p> <p>Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets.</p> <p>Results</p> <p>Here we explore the phylogenetic signal present in molecular data by genomic signatures, defined as the set of frequencies of short oligonucleotides present in DNA sequences. Although violating many of the standard assumptions of traditional phylogenetic analyses – in particular explicit statements of homology inherent in character matrices – the use of the signature does permit the analysis of very long sequences, even those that are unalignable, and is therefore most useful in cases where alignment is questionable. We compare the results obtained by traditional phylogenetic methods to those inferred by the signature method for two genes: RAG1, which is easily alignable, and 18S RNA, where alignments are often ambiguous for some regions. We also apply this method to a multigene data set of 33 genes for 9 bacteria and one archea species as well as to the whole genome of a set of 16 γ-proteobacteria. In addition to delivering phylogenetic results comparable to traditional methods, the comparison of signatures for the sequences involved in the bacterial example identified putative candidates for horizontal gene transfers.</p> <p>Conclusion</p> <p>The signature method is therefore a fast tool for exploring phylogenetic data, providing not only a pretreatment for discovering new sequence relationships, but also for identifying cases of sequence evolution that could confound traditional phylogenetic analysis.</p>http://www.biomedcentral.com/1471-2148/5/63 |
| spellingShingle | Giron Alain Edwards Scott Dufraigne Christine Chapus Charles Fertil Bernard Deschavanne Patrick Exploration of phylogenetic data using a global sequence analysis method BMC Evolutionary Biology |
| title | Exploration of phylogenetic data using a global sequence analysis method |
| title_full | Exploration of phylogenetic data using a global sequence analysis method |
| title_fullStr | Exploration of phylogenetic data using a global sequence analysis method |
| title_full_unstemmed | Exploration of phylogenetic data using a global sequence analysis method |
| title_short | Exploration of phylogenetic data using a global sequence analysis method |
| title_sort | exploration of phylogenetic data using a global sequence analysis method |
| url | http://www.biomedcentral.com/1471-2148/5/63 |
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