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dc.contributor.author
Szalkowski, Adam M.
dc.contributor.author
Anisimova, Maria
dc.date.accessioned
2019-04-02T16:19:17Z
dc.date.available
2017-06-10T22:29:23Z
dc.date.available
2019-04-02T16:16:34Z
dc.date.available
2019-04-02T16:19:17Z
dc.date.issued
2013-09
dc.identifier.other
10.1093/nar/gkt628
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/72947
dc.identifier.doi
10.3929/ethz-b-000072947
dc.description.abstract
Tandem repeats (TRs) are often present in proteins with crucial functions, responsible for resistance, pathogenicity and associated with infectious or neurodegenerative diseases. This motivates numerous studies of TRs and their evolution, requiring accurate multiple sequence alignment. TRs may be lost or inserted at any position of a TR region by replication slippage or recombination, but current methods assume fixed unit boundaries, and yet are of high complexity. We present a new global graph-based alignment method that does not restrict TR unit indels by unit boundaries. TR indels are modeled separately and penalized using the phylogeny-aware alignment algorithm. This ensures enhanced accuracy of reconstructed alignments, disentangling TRs and measuring indel events and rates in a biologically meaningful way. Our method detects not only duplication events but also all changes in TR regions owing to recombination, strand slippage and other events inserting or deleting TR units. We evaluate our method by simulation incorporating TR evolution, by either sampling TRs from a profile hidden Markov model or by mimicking strand slippage with duplications. The new method is illustrated on a family of type III effectors, a pathogenicity determinant in agriculturally important bacteria Ralstonia solanacearum. We show that TR indel rate variation contributes to the diversification of this protein family.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
Oxford University Press
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/3.0/
dc.title
Graph-based modeling of tandem repeats improves global multiple sequence alignment
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 3.0 Unported
dc.date.published
2013-07-22
ethz.journal.title
Nucleic acids research
ethz.journal.volume
41
en_US
ethz.journal.issue
17
en_US
ethz.pages.start
e162
en_US
ethz.size
11 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.nebis
000038633
ethz.publication.place
Oxford
en_US
ethz.publication.status
published
en_US
ethz.date.deposited
2017-06-10T22:31:00Z
ethz.source
ECIT
ethz.identifier.importid
imp593651122408a73785
ethz.ecitpid
pub:115563
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2017-07-12T10:43:22Z
ethz.rosetta.lastUpdated
2019-04-02T16:19:38Z
ethz.rosetta.exportRequired
true
ethz.rosetta.versionExported
true
ethz.COinS
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