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Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes
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ISSN: 1545-5963
| ASCII Text | x | ||
| Pedro Feijao, Joao Meidanis, "Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 99, no. 1, pp. 1, , 5555. | |||
| BibTex | x | ||
| @article{ 10.1109/TCBB.2012.161, author = {Pedro Feijao and Joao Meidanis}, title = {Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {99}, number = {1}, issn = {1545-5963}, year = {5555}, pages = {1}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.161}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, } | |||
| RefWorks Procite/RefMan/Endnote | x | ||
| TY - JOUR JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics TI - Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes IS - 1 SN - 1545-5963 SP EP EPD - 1 A1 - Pedro Feijao, A1 - Joao Meidanis, PY - 5555 KW - Biology and genetics KW - Theory of Computation KW - Analysis of Algorithms and Problem Complexity KW - Computer Applications KW - Life and Medical Sciences VL - 99 JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics ER - | |||
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.161
Algebraic rearrangement theory, as introduced by Meidanis and Dias, focuses on representing the order in which genes appear in chromosomes, and applies to circular chromosomes only. By shifting our attention to genome adjacencies, we introduce the adjacency algebraic theory, extending the original algebraic theory to linear chromosomes in a very natural way, also allowing the original algebraic distance formula to be used to the general multichromosomal case, with both linear and circular chromosomes. The resulting distance, which we call algebraic distance here, is very similar to, but not quite the same as, DCJ distance. We present linear time algorithms to compute it and to sort genomes. We show how to compute the rearrangement distance from the adjacency graph, for an easier comparison with other rearrangement distances. A thorough discussion on the relationship between the chromosomal and adjacency representation is also given, and we show how all classic rearrangement operations can be modeled using the algebraic theory.
Index Terms:
Biology and genetics,Theory of Computation,Analysis of Algorithms and Problem Complexity,Computer Applications,Life and Medical Sciences
Citation:
Pedro Feijao, Joao Meidanis, "Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11 Dec. 2012. IEEE computer Society Digital Library. IEEE Computer Society, <http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.161>
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