ArticleGenome research2003
LineUp: statistical detection of chromosomal homology with application to plant comparative genomics.
Article in Genome research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Accurate Inference of the Polyploid Continuum Using Forward-Time Simulations.Molecular biology and evolution · 2024Article
- Review
- Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes.PLoS computational biology · 2015Article
- PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees.BMC bioinformatics · 2014Article
- SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes.PloS one · 2014Article
- Locally duplicated ohnologs evolve faster than nonlocally duplicated ohnologs in Arabidopsis and rice.Genome biology and evolution · 2013Article
- MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.Nucleic acids research · 2012Article
- i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets.Nucleic acids research · 2012Article
- Article
- Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection.Functional & integrative genomics · 2009Article
- CHSMiner: a GUI tool to identify chromosomal homologous segments.Algorithms for molecular biology : AMB · 2009Article
- Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora.Genome biology · 2009Article
- Precise detection of rearrangement breakpoints in mammalian chromosomes.BMC bioinformatics · 2008Article
- Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution.The Plant cell · 2008Article
- Two paralogous genes encoding small subunits of ADP-glucose pyrophosphorylase in maize, Bt2 and L2, replace the single alternatively spliced gene found in other cereal species.Journal of molecular evolution · 2007Article
- SyMAP: A system for discovering and viewing syntenic regions of FPC maps.Genome research · 2006Article
- How can we use genomics to improve cereals with rice as a reference genome?Plant molecular biology · 2005Article
- Statistical evidence for a more than 800-million-year-old evolutionarily conserved genomic region in our genome.Journal of molecular evolution · 2004Article
- Building genomic profiles for uncovering segmental homology in the twilight zone.Genome research · 2004Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The identification of homologous regions between chromosomes forms the basis for studies of genome organization, comparative genomics, and evolutionary genomics. Identification of these regions can be based on either synteny or colinearity, but there are few methods to test statistically for significant evidence of homology. In the present study, we improve a preexisting method that used colinearity as the basis for statistical tests. Improvements include computational efficiency and a relaxation of the colinearity assumption. Two algorithms perform the method: FullPermutation, which searches exhaustively for runs of markers, and FastRuns, which trades faster run times for exhaustive searches. The algorithms described here are available in the LineUp package (http://www.igb.uci.edu/ approximately baldig/lineup). We explore the performance of both algorithms on simulated data and also on genetic map data from maize (Zea mays ssp. mays). The method has reasonable power to detect a homologous region; for example, in >90% of simulations, both algorithms detect a homologous region of 10 markers buried in a random background, even when the homologous regions have diverged by numerous inversion events. The methods were applied to four maize molecular maps. All maps indicate that the maize genome contains extensive regions of genomic duplication and multiplication. Nonetheless, maps differ substantially in the location of homologous regions, probably reflecting the incomplete nature of genetic map data. The variation among maps has important implications for evolutionary inference from genetic map data.
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