A method for determining the position and size of optimal sequence regions for phylogenetic analysis
The availability of fast and accurate sequencing procedures along with the use of PCR has led to a proliferation of studies of variability at the molecular level in populations. Nevertheless, it is often impractical to examine long genomic stretches and a large number of individuals at the same time. In order to optimize this kind of study, we suggest a heuristic procedure for detection of the shortest region whose informational content can be considered sufficient for significant phylogenetic reconstruction. The method is based on the comparison of the pairwise genetic distances obtained from a set of sequences of reference to those obtained for different windows of variable size and position by means of a simple index. We also present an approach for testing whether the informative content in the stretches selected in this way is significantly different from the corresponding content shown by the larger genomic regions used as reference. Application of this test to the analysis of the VP1 protein gene of foot-and-mouth-disease type C virus allowed us to define optimal stretches whose informative content is not significantly different from that displayed by the complete VP1 sequence. We showed that the predictions made for type C sequences are valid for type O sequences, indicating that the results of the procedure are consistent. © 1995, Springer-Verlag New York Inc. All rights reserved.
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1995
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Subjects: | Phylogeny, Neighbor-Joining method, Bootstrap, Optimal size, Non-random sequence, Information, Foot-and-mouth disease virus, |
Online Access: | http://hdl.handle.net/20.500.12792/2659 http://hdl.handle.net/10261/293658 |
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dig-inia-es-10261-2936582023-02-20T10:30:41Z A method for determining the position and size of optimal sequence regions for phylogenetic analysis Martin, M. J. González-Candelas, F. Sobrino, F. Dopazo, J. Phylogeny Neighbor-Joining method Bootstrap Optimal size Non-random sequence Information Foot-and-mouth disease virus The availability of fast and accurate sequencing procedures along with the use of PCR has led to a proliferation of studies of variability at the molecular level in populations. Nevertheless, it is often impractical to examine long genomic stretches and a large number of individuals at the same time. In order to optimize this kind of study, we suggest a heuristic procedure for detection of the shortest region whose informational content can be considered sufficient for significant phylogenetic reconstruction. The method is based on the comparison of the pairwise genetic distances obtained from a set of sequences of reference to those obtained for different windows of variable size and position by means of a simple index. We also present an approach for testing whether the informative content in the stretches selected in this way is significantly different from the corresponding content shown by the larger genomic regions used as reference. Application of this test to the analysis of the VP1 protein gene of foot-and-mouth-disease type C virus allowed us to define optimal stretches whose informative content is not significantly different from that displayed by the complete VP1 sequence. We showed that the predictions made for type C sequences are valid for type O sequences, indicating that the results of the procedure are consistent. © 1995, Springer-Verlag New York Inc. All rights reserved. 2023-02-20T10:30:41Z 2023-02-20T10:30:41Z 1995 journal article Journal of Molecular Evolution 41: 1128-1138 (1995) 0022-2844 http://hdl.handle.net/20.500.12792/2659 http://hdl.handle.net/10261/293658 10.1007/BF00173194 1432-1432 en none Springer |
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Phylogeny Neighbor-Joining method Bootstrap Optimal size Non-random sequence Information Foot-and-mouth disease virus Phylogeny Neighbor-Joining method Bootstrap Optimal size Non-random sequence Information Foot-and-mouth disease virus |
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Phylogeny Neighbor-Joining method Bootstrap Optimal size Non-random sequence Information Foot-and-mouth disease virus Phylogeny Neighbor-Joining method Bootstrap Optimal size Non-random sequence Information Foot-and-mouth disease virus Martin, M. J. González-Candelas, F. Sobrino, F. Dopazo, J. A method for determining the position and size of optimal sequence regions for phylogenetic analysis |
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The availability of fast and accurate sequencing procedures along with the use of PCR has led to a proliferation of studies of variability at the molecular level in populations. Nevertheless, it is often impractical to examine long genomic stretches and a large number of individuals at the same time. In order to optimize this kind of study, we suggest a heuristic procedure for detection of the shortest region whose informational content can be considered sufficient for significant phylogenetic reconstruction. The method is based on the comparison of the pairwise genetic distances obtained from a set of sequences of reference to those obtained for different windows of variable size and position by means of a simple index. We also present an approach for testing whether the informative content in the stretches selected in this way is significantly different from the corresponding content shown by the larger genomic regions used as reference. Application of this test to the analysis of the VP1 protein gene of foot-and-mouth-disease type C virus allowed us to define optimal stretches whose informative content is not significantly different from that displayed by the complete VP1 sequence. We showed that the predictions made for type C sequences are valid for type O sequences, indicating that the results of the procedure are consistent. © 1995, Springer-Verlag New York Inc. All rights reserved. |
format |
journal article |
topic_facet |
Phylogeny Neighbor-Joining method Bootstrap Optimal size Non-random sequence Information Foot-and-mouth disease virus |
author |
Martin, M. J. González-Candelas, F. Sobrino, F. Dopazo, J. |
author_facet |
Martin, M. J. González-Candelas, F. Sobrino, F. Dopazo, J. |
author_sort |
Martin, M. J. |
title |
A method for determining the position and size of optimal sequence regions for phylogenetic analysis |
title_short |
A method for determining the position and size of optimal sequence regions for phylogenetic analysis |
title_full |
A method for determining the position and size of optimal sequence regions for phylogenetic analysis |
title_fullStr |
A method for determining the position and size of optimal sequence regions for phylogenetic analysis |
title_full_unstemmed |
A method for determining the position and size of optimal sequence regions for phylogenetic analysis |
title_sort |
method for determining the position and size of optimal sequence regions for phylogenetic analysis |
publisher |
Springer |
publishDate |
1995 |
url |
http://hdl.handle.net/20.500.12792/2659 http://hdl.handle.net/10261/293658 |
work_keys_str_mv |
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