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Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes

Published on Dec 1, 2017in BMC Bioinformatics2.51
· DOI :10.1186/s12859-017-1529-8
Malte Petersen11
Estimated H-index: 11
,
Karen Meusemann19
Estimated H-index: 19
(University of Freiburg)
+ 8 AuthorsOliver Niehuis22
Estimated H-index: 22
(University of Freiburg)
Abstract
Background Orthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An accurate orthology assignment is a crucial step for comparative genomic studies. Orthologous genes in two organisms can be identified by applying a so-called reciprocal search strategy, given that complete information of the organisms’ gene repertoire is available. In many investigations, however, only a fraction of the gene content of the organisms under study is examined (e.g., RNA sequencing). Here, identification of orthologous nucleotide or amino acid sequences can be achieved using a graph-based approach that maps nucleotide sequences to genes of known orthology. Existing implementations of this approach, however, suffer from algorithmic issues that may cause problems in downstream analyses.
  • References (25)
  • Citations (26)
References25
Newest
#1Evgenia V. Kriventseva (Swiss Institute of Bioinformatics)H-Index: 29
#2Fredrik Tegenfeldt (Swiss Institute of Bioinformatics)H-Index: 6
Last.Evgeny M. Zdobnov (Swiss Institute of Bioinformatics)H-Index: 55
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#1Adrian M. Altenhoff (Swiss Institute of Bioinformatics)H-Index: 16
#2Nives Škunca (Swiss Institute of Bioinformatics)H-Index: 15
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#2Amhed Missael (University of Texas at Austin)H-Index: 1
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#1James F. Denton (IU: Indiana University Bloomington)H-Index: 1
#2Jose Lugo-Martinez (IU: Indiana University Bloomington)H-Index: 6
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#1Salvador Capella-Gutiérrez (TUK: Kaiserslautern University of Technology)H-Index: 18
#2Frank Kauff (TUK: Kaiserslautern University of Technology)H-Index: 26
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#2Till-Hendrik Macher (University of Duisburg-Essen)H-Index: 1
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#1Aleš Buček (OIST: Okinawa Institute of Science and Technology)H-Index: 4
#2Jan Šobotník (CULS: Czech University of Life Sciences Prague)H-Index: 19
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#1Karen Meusemann (University of Freiburg)H-Index: 19
#2Judith Korb (University of Freiburg)H-Index: 27
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#1J. Pflug (OSU: Oregon State University)
#2J. S. Johnston (A&M: Texas A&M University)
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#1Rachel Skinner (UIUC: University of Illinois at Urbana–Champaign)
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