The ABCs of MGR with DCJ
We study the small phylogeny problem in the space of multichromosomal genomes under the double cut and join metric. This is similar to the existing MGR (multiple genome rearrangements) approach but it allows, in addition to inversion and reciprocal translocation, operations of transposition and bloc...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2008-01-01
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| Series: | Evolutionary Bioinformatics |
| Online Access: | https://doi.org/10.1177/117693430800400004 |
| _version_ | 1819169102123499520 |
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| author | Zaky Adam David Sankoff |
| author_facet | Zaky Adam David Sankoff |
| author_sort | Zaky Adam |
| collection | DOAJ |
| description | We study the small phylogeny problem in the space of multichromosomal genomes under the double cut and join metric. This is similar to the existing MGR (multiple genome rearrangements) approach but it allows, in addition to inversion and reciprocal translocation, operations of transposition and block interchange. Empirically, with chloroplast and mammalian data sets, it finds solutions as good as or better than MGR when the latter operations are prohibited. Permitting these operations allows quantitatively better solutions where part of the reconstructed ancestral genomes may be included in circular chromosomes. We discuss the biological likelihood of transpositions and block interchanges in the mammalian data. |
| first_indexed | 2024-12-22T19:14:09Z |
| format | Article |
| id | doaj.art-fea8aa8e03ea43118678e91ddc8bf256 |
| institution | Directory Open Access Journal |
| issn | 1176-9343 |
| language | English |
| last_indexed | 2024-12-22T19:14:09Z |
| publishDate | 2008-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Evolutionary Bioinformatics |
| spelling | doaj.art-fea8aa8e03ea43118678e91ddc8bf2562022-12-21T18:15:35ZengSAGE PublishingEvolutionary Bioinformatics1176-93432008-01-01410.1177/117693430800400004The ABCs of MGR with DCJZaky Adam0David Sankoff1School of Information Technology and Engineering, University of Ottawa, Ottawa, Canada, K1N 6N5.Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, ON, Canada, K1N 6N5.We study the small phylogeny problem in the space of multichromosomal genomes under the double cut and join metric. This is similar to the existing MGR (multiple genome rearrangements) approach but it allows, in addition to inversion and reciprocal translocation, operations of transposition and block interchange. Empirically, with chloroplast and mammalian data sets, it finds solutions as good as or better than MGR when the latter operations are prohibited. Permitting these operations allows quantitatively better solutions where part of the reconstructed ancestral genomes may be included in circular chromosomes. We discuss the biological likelihood of transpositions and block interchanges in the mammalian data.https://doi.org/10.1177/117693430800400004 |
| spellingShingle | Zaky Adam David Sankoff The ABCs of MGR with DCJ Evolutionary Bioinformatics |
| title | The ABCs of MGR with DCJ |
| title_full | The ABCs of MGR with DCJ |
| title_fullStr | The ABCs of MGR with DCJ |
| title_full_unstemmed | The ABCs of MGR with DCJ |
| title_short | The ABCs of MGR with DCJ |
| title_sort | abcs of mgr with dcj |
| url | https://doi.org/10.1177/117693430800400004 |
| work_keys_str_mv | AT zakyadam theabcsofmgrwithdcj AT davidsankoff theabcsofmgrwithdcj AT zakyadam abcsofmgrwithdcj AT davidsankoff abcsofmgrwithdcj |