Aligning two genomic sequences that contain duplications

Minmei Hou; Cathy Riemer; Piotr Berman; Ross C. Hardison; Webb Miller

doi:10.1007/978-3-642-04744-2_9

Aligning two genomic sequences that contain duplications

Minmei Hou, Cathy Riemer, Piotr Berman, Ross C. Hardison, Webb Miller

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

1 Scopus citations

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 language	English (US)
Title of host publication	Comparative Genomics - International Workshop, RECOMB-CG 2009, Proceedings
Pages	98-110
Number of pages	13
DOIs	https://doi.org/10.1007/978-3-642-04744-2_9
State	Published - 2009
Event	7th International Workshop on Comparative Genomics, RECOMB-CG 2009 - Budapest, Hungary Duration: Sep 27 2009 → Sep 29 2009

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	5817 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	7th International Workshop on Comparative Genomics, RECOMB-CG 2009
Country/Territory	Hungary
City	Budapest
Period	9/27/09 → 9/29/09

All Science Journal Classification (ASJC) codes

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-642-04744-2_9

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

@inproceedings{887e7d24109e476296ef13963cac36c2,

title = "Aligning two genomic sequences that contain duplications",

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.",

author = "Minmei Hou and Cathy Riemer and Piotr Berman and Hardison, {Ross C.} and Webb Miller",

year = "2009",

doi = "10.1007/978-3-642-04744-2_9",

language = "English (US)",

isbn = "3642047432",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

pages = "98--110",

booktitle = "Comparative Genomics - International Workshop, RECOMB-CG 2009, Proceedings",

note = "7th International Workshop on Comparative Genomics, RECOMB-CG 2009 ; Conference date: 27-09-2009 Through 29-09-2009",

}

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 et al.
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 proceeding › Conference contribution

TY - GEN

T1 - Aligning two genomic sequences that contain duplications

AU - Hou, Minmei

AU - Riemer, Cathy

AU - Berman, Piotr

AU - Hardison, Ross C.

AU - Miller, Webb

PY - 2009

Y1 - 2009

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=78651242141&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=78651242141&partnerID=8YFLogxK

U2 - 10.1007/978-3-642-04744-2_9

DO - 10.1007/978-3-642-04744-2_9

M3 - Conference contribution

AN - SCOPUS:78651242141

SN - 3642047432

SN - 9783642047435

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 98

EP - 110

BT - Comparative Genomics - International Workshop, RECOMB-CG 2009, Proceedings

T2 - 7th International Workshop on Comparative Genomics, RECOMB-CG 2009

Y2 - 27 September 2009 through 29 September 2009

ER -

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)). doi: 10.1007/978-3-642-04744-2_9

Aligning two genomic sequences that contain duplications

Abstract

Publication series

Other

All Science Journal Classification (ASJC) codes

Access to Document

Other files and links

Fingerprint

Cite this