UniMoG—a unifying framework for genomic distance calculation and sorting based on DCJ

Summary: UniMoG is a software combining five genome rearrangement models: double cut and join (DCJ), restricted DCJ, Hannenhalli and Pevzner (HP), inversion and translocation. It can compute the pairwise genomic distances and a corresponding optimal sorting scenario for an arbitrary number of genome...

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Detalles Bibliográficos
Autores principales: Hilker, Rolf, Sickinger, Corinna, Pedersen, Christian N.S., Stoye, Jens
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463123/
https://www.ncbi.nlm.nih.gov/pubmed/22815356
http://dx.doi.org/10.1093/bioinformatics/bts440
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author Hilker, Rolf
Sickinger, Corinna
Pedersen, Christian N.S.
Stoye, Jens
author_facet Hilker, Rolf
Sickinger, Corinna
Pedersen, Christian N.S.
Stoye, Jens
author_sort Hilker, Rolf
collection PubMed
description Summary: UniMoG is a software combining five genome rearrangement models: double cut and join (DCJ), restricted DCJ, Hannenhalli and Pevzner (HP), inversion and translocation. It can compute the pairwise genomic distances and a corresponding optimal sorting scenario for an arbitrary number of genomes. All five models can be unified through the DCJ model, thus the implementation is based on DCJ and, where reasonable, uses the most efficient existing algorithms for each distance and sorting problem. Both textual and graphical output is possible for visualizing the operations. Availability and implementation: The software is available through the Bielefeld University Bioinformatics Web Server at http://bibiserv.techfak.uni-bielefeld.de/dcj with instructions and example data. Contact: rhilker@cebitec.uni-bielefeld.de
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spelling pubmed-34631232012-12-12 UniMoG—a unifying framework for genomic distance calculation and sorting based on DCJ Hilker, Rolf Sickinger, Corinna Pedersen, Christian N.S. Stoye, Jens Bioinformatics Applications Notes Summary: UniMoG is a software combining five genome rearrangement models: double cut and join (DCJ), restricted DCJ, Hannenhalli and Pevzner (HP), inversion and translocation. It can compute the pairwise genomic distances and a corresponding optimal sorting scenario for an arbitrary number of genomes. All five models can be unified through the DCJ model, thus the implementation is based on DCJ and, where reasonable, uses the most efficient existing algorithms for each distance and sorting problem. Both textual and graphical output is possible for visualizing the operations. Availability and implementation: The software is available through the Bielefeld University Bioinformatics Web Server at http://bibiserv.techfak.uni-bielefeld.de/dcj with instructions and example data. Contact: rhilker@cebitec.uni-bielefeld.de Oxford University Press 2012-10-01 2012-07-18 /pmc/articles/PMC3463123/ /pubmed/22815356 http://dx.doi.org/10.1093/bioinformatics/bts440 Text en © The Author 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Hilker, Rolf
Sickinger, Corinna
Pedersen, Christian N.S.
Stoye, Jens
UniMoG—a unifying framework for genomic distance calculation and sorting based on DCJ
title UniMoG—a unifying framework for genomic distance calculation and sorting based on DCJ
title_full UniMoG—a unifying framework for genomic distance calculation and sorting based on DCJ
title_fullStr UniMoG—a unifying framework for genomic distance calculation and sorting based on DCJ
title_full_unstemmed UniMoG—a unifying framework for genomic distance calculation and sorting based on DCJ
title_short UniMoG—a unifying framework for genomic distance calculation and sorting based on DCJ
title_sort unimog—a unifying framework for genomic distance calculation and sorting based on dcj
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463123/
https://www.ncbi.nlm.nih.gov/pubmed/22815356
http://dx.doi.org/10.1093/bioinformatics/bts440
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