Alignment and analysis of closely related genomes

Allison Regier; Michael Olson; Scott J. Emrich

doi:10.1007/978-3-642-00727-9_32

Alignment and analysis of closely related genomes

Allison Regier, Michael Olson, Scott J. Emrich

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

Complex strategies have been developed for whole genome alignment of multiple species. In the case of population genomics studies, the sequences being aligned are often very similar.We propose a reference coordinate system that simplifies the task of comparing many closely related genomes while taking into account structural rearrangements.We implemented software to compare a group of three strains of the malaria mosquito, Anopheles gambiae and a group of three strains of the malaria parasite, Plasmodium falciparum. Our simplified representation enables us to leverage existing work on the species while performing fine-grained analysis on the new draft genomes. Further, this approach will easily scale to hundreds of closely related genomes, enabling new analyses in population genomics as additional genomic sequences become available.

Original language	English
Title of host publication	Bioinformatics and Computational Biology - First International Conference, BICoB 2009, Proceedings
Pages	343-352
Number of pages	10
DOIs	https://doi.org/10.1007/978-3-642-00727-9_32
State	Published - 2009
Externally published	Yes
Event	1st International Conference on Bioinformatics and Computational Biology, BICoB 2009 - New Orleans, LA, United States Duration: Apr 8 2009 → Apr 10 2009

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	5462 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	1st International Conference on Bioinformatics and Computational Biology, BICoB 2009
Country/Territory	United States
City	New Orleans, LA
Period	04/8/09 → 04/10/09

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10.1007/978-3-642-00727-9_32

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Regier, A., Olson, M., & Emrich, S. J. (2009). Alignment and analysis of closely related genomes. In Bioinformatics and Computational Biology - First International Conference, BICoB 2009, Proceedings (pp. 343-352). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5462 LNBI). https://doi.org/10.1007/978-3-642-00727-9_32

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title = "Alignment and analysis of closely related genomes",

abstract = "Complex strategies have been developed for whole genome alignment of multiple species. In the case of population genomics studies, the sequences being aligned are often very similar.We propose a reference coordinate system that simplifies the task of comparing many closely related genomes while taking into account structural rearrangements.We implemented software to compare a group of three strains of the malaria mosquito, Anopheles gambiae and a group of three strains of the malaria parasite, Plasmodium falciparum. Our simplified representation enables us to leverage existing work on the species while performing fine-grained analysis on the new draft genomes. Further, this approach will easily scale to hundreds of closely related genomes, enabling new analyses in population genomics as additional genomic sequences become available.",

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Regier, A, Olson, M & Emrich, SJ 2009, Alignment and analysis of closely related genomes. in Bioinformatics and Computational Biology - First International Conference, BICoB 2009, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 5462 LNBI, pp. 343-352, 1st International Conference on Bioinformatics and Computational Biology, BICoB 2009, New Orleans, LA, United States, 04/8/09. https://doi.org/10.1007/978-3-642-00727-9_32

Alignment and analysis of closely related genomes. / Regier, Allison; Olson, Michael; Emrich, Scott J.
Bioinformatics and Computational Biology - First International Conference, BICoB 2009, Proceedings. 2009. p. 343-352 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5462 LNBI).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AB - Complex strategies have been developed for whole genome alignment of multiple species. In the case of population genomics studies, the sequences being aligned are often very similar.We propose a reference coordinate system that simplifies the task of comparing many closely related genomes while taking into account structural rearrangements.We implemented software to compare a group of three strains of the malaria mosquito, Anopheles gambiae and a group of three strains of the malaria parasite, Plasmodium falciparum. Our simplified representation enables us to leverage existing work on the species while performing fine-grained analysis on the new draft genomes. Further, this approach will easily scale to hundreds of closely related genomes, enabling new analyses in population genomics as additional genomic sequences become available.

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Regier A, Olson M, Emrich SJ. Alignment and analysis of closely related genomes. In Bioinformatics and Computational Biology - First International Conference, BICoB 2009, Proceedings. 2009. p. 343-352. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-642-00727-9_32

Alignment and analysis of closely related genomes

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