Aligning two genomic sequences that contain duplications

Minmei Hou, Cathy Riemer, Piotr Berman, Ross Cameron Hardison, Webb Miller

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

It is difficult to properly align genomic sequences that contain intra-species duplications. With this goal in mind, we have developed a tool, called TOAST (two-way orthologous alignment selection tool), for predicting whether two aligned regions from different species are orthologous, i.e., separated by a speciation event, as opposed to a duplication event. The advantage of restricting alignment to orthologous pairs is that they constitute the aligning regions that are most likely to share the same biological function, and most easily analyzed for evidence of selection. We evaluate TOAST on 12 human/mouse gene clusters.

Original languageEnglish (US)
Title of host publicationComparative Genomics - International Workshop, RECOMB-CG 2009, Proceedings
Pages98-110
Number of pages13
DOIs
StatePublished - Dec 1 2009
Event7th International Workshop on Comparative Genomics, RECOMB-CG 2009 - Budapest, Hungary
Duration: Sep 27 2009Sep 29 2009

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5817 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other7th International Workshop on Comparative Genomics, RECOMB-CG 2009
CountryHungary
CityBudapest
Period9/27/099/29/09

Fingerprint

Duplication
Genomics
Alignment
Speciation
Mouse
Genes
Likely
Gene
Evaluate

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Hou, M., Riemer, C., Berman, P., Hardison, R. C., & Miller, W. (2009). Aligning two genomic sequences that contain duplications. In Comparative Genomics - International Workshop, RECOMB-CG 2009, Proceedings (pp. 98-110). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5817 LNBI). https://doi.org/10.1007/978-3-642-04744-2_9
Hou, Minmei ; Riemer, Cathy ; Berman, Piotr ; Hardison, Ross Cameron ; Miller, Webb. / Aligning two genomic sequences that contain duplications. Comparative Genomics - International Workshop, RECOMB-CG 2009, Proceedings. 2009. pp. 98-110 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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Hou, M, Riemer, C, Berman, P, Hardison, RC & Miller, W 2009, Aligning two genomic sequences that contain duplications. in Comparative Genomics - International Workshop, RECOMB-CG 2009, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 5817 LNBI, pp. 98-110, 7th International Workshop on Comparative Genomics, RECOMB-CG 2009, Budapest, Hungary, 9/27/09. https://doi.org/10.1007/978-3-642-04744-2_9

Aligning two genomic sequences that contain duplications. / Hou, Minmei; Riemer, Cathy; Berman, Piotr; Hardison, Ross Cameron; Miller, Webb.

Comparative Genomics - International Workshop, RECOMB-CG 2009, Proceedings. 2009. p. 98-110 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5817 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Hou M, Riemer C, Berman P, Hardison RC, Miller W. Aligning two genomic sequences that contain duplications. In Comparative Genomics - International Workshop, RECOMB-CG 2009, Proceedings. 2009. p. 98-110. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-642-04744-2_9