COMPAM: Visualization of combining pairwise alignments for multiple genomes

Do Hoon Lee; Jeong Hyeon Choi; Mehmet M. Dalkilic; Sun Kim

doi:10.1093/bioinformatics/bti759

COMPAM: Visualization of combining pairwise alignments for multiple genomes

Do Hoon Lee, Jeong Hyeon Choi, Mehmet M. Dalkilic, Sun Kim

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

Abstract

Summary: COMPAM is a tool for visualizing relationships among multiple whole genomes by combining all pairwise genome alignments. It displays shared conserved regions (blocks) and where these blocks occur (edges) as block relation graphs which can be explored interactively. An unannotated genome, e.g. can then be explored using information from well-annotated genomes, COG-based genome annotation and genes. COMPAM can run either as a stand-alone application or through an applet that is provided as service to PLATCOM, a toolset for whole genome comparative analysis, where a wide variety of genomes can be easily selected. Features provided by COMPAM include the ability to export genome relationship information into file formats that can be used by other existing tools.

Original language	English (US)
Pages (from-to)	242-244
Number of pages	3
Journal	Bioinformatics
Volume	22
Issue number	2
DOIs	https://doi.org/10.1093/bioinformatics/bti759
State	Published - Jan 15 2006
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/bti759

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@article{f34758fedeca4131b0765934a147aa73,

title = "COMPAM: Visualization of combining pairwise alignments for multiple genomes",

abstract = "Summary: COMPAM is a tool for visualizing relationships among multiple whole genomes by combining all pairwise genome alignments. It displays shared conserved regions (blocks) and where these blocks occur (edges) as block relation graphs which can be explored interactively. An unannotated genome, e.g. can then be explored using information from well-annotated genomes, COG-based genome annotation and genes. COMPAM can run either as a stand-alone application or through an applet that is provided as service to PLATCOM, a toolset for whole genome comparative analysis, where a wide variety of genomes can be easily selected. Features provided by COMPAM include the ability to export genome relationship information into file formats that can be used by other existing tools.",

author = "Lee, {Do Hoon} and Choi, {Jeong Hyeon} and Dalkilic, {Mehmet M.} and Sun Kim",

note = "Funding Information: We thank Kwangmin Choi for his suggestions and comments. We also appreciate anonymous reviewers{\textquoteright} comments which improved the previous version of the paper significantly. This work is partially supported by NSF CAREER Award DBI-0237901 to S.K., NSF IIS-0082401 to M.M.D. and overseas research fund of Miryang National University to D.H.L.",

year = "2006",

month = jan,

day = "15",

doi = "10.1093/bioinformatics/bti759",

language = "English (US)",

volume = "22",

pages = "242--244",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "2",

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T1 - COMPAM

T2 - Visualization of combining pairwise alignments for multiple genomes

AU - Lee, Do Hoon

AU - Choi, Jeong Hyeon

AU - Dalkilic, Mehmet M.

AU - Kim, Sun

N1 - Funding Information: We thank Kwangmin Choi for his suggestions and comments. We also appreciate anonymous reviewers’ comments which improved the previous version of the paper significantly. This work is partially supported by NSF CAREER Award DBI-0237901 to S.K., NSF IIS-0082401 to M.M.D. and overseas research fund of Miryang National University to D.H.L.

PY - 2006/1/15

Y1 - 2006/1/15

N2 - Summary: COMPAM is a tool for visualizing relationships among multiple whole genomes by combining all pairwise genome alignments. It displays shared conserved regions (blocks) and where these blocks occur (edges) as block relation graphs which can be explored interactively. An unannotated genome, e.g. can then be explored using information from well-annotated genomes, COG-based genome annotation and genes. COMPAM can run either as a stand-alone application or through an applet that is provided as service to PLATCOM, a toolset for whole genome comparative analysis, where a wide variety of genomes can be easily selected. Features provided by COMPAM include the ability to export genome relationship information into file formats that can be used by other existing tools.

AB - Summary: COMPAM is a tool for visualizing relationships among multiple whole genomes by combining all pairwise genome alignments. It displays shared conserved regions (blocks) and where these blocks occur (edges) as block relation graphs which can be explored interactively. An unannotated genome, e.g. can then be explored using information from well-annotated genomes, COG-based genome annotation and genes. COMPAM can run either as a stand-alone application or through an applet that is provided as service to PLATCOM, a toolset for whole genome comparative analysis, where a wide variety of genomes can be easily selected. Features provided by COMPAM include the ability to export genome relationship information into file formats that can be used by other existing tools.

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COMPAM: Visualization of combining pairwise alignments for multiple genomes

Abstract

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