DAGchainer: a tool for mining segmental genome duplications and synteny

By Brian J. Haas, Arthur L. Delcher, Jennifer R. Wortman, Steven L. Salzberg. Bioinform., 2004

385 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/bd9447770801a08240805c2da934453e825a44cc

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Citations in the corpus

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea (2011, methodology): “To build syntenic regions between genomes, we used DAGchainer [27] to identify blocks of four or more orthologous BDBH gene pairs.”
SyMAP v3.4: a turnkey synteny system with application to plant genomes (2011, methodology): “When comparing two genomes, an algorithm may detect homologous genes with conserved order, for which the following terms have been used: microcolinearity [ADHoRe (18)]; colinearity [DAGc hainer (19) and ColinearScan (20)]; locally collinear blocks [Mauve (21)]; and conserved synteny [CYNTENATOR (22)”
An Integrated Pipeline for de Novo Assembly of Microbial Genomes (2012, methodology): “Chaining algorithms such as FISH [23] and DAGChainer [24], are not permissive for this task, as they depend on a collinear arrangement of points.”
Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. (2017, background): “0 (Wang et al., 2010) https://sourceforge.net/projects/ kakscalculator2/ BLASTZ (Schwartz et al., 2003) genomewiki.ucsc.edu/index.php/Blastz DAGchainer (Haas et al., 2004) http://dagchainer.sourceforge.net/ SynMap at CoGe website (Lyons et al., 2008) https://genomevolution.org/CoGe/SynMap.pl Transpo”
The TIGR Rice Genome Annotation Resource: improvements and new features (2006, methodology): “This analysis utilized the DAGChainer program (30,32) with parameters 100 and 500 kb for maximum distance allowed between two collinear gene pairs in order to identify segmentally duplicated genes.”
Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. (2009, methodology): “Figure 2b is an Arabidopsis-Arabidopsis sequence comparison dotplot driven by the DAGchainer algorithm (41), downloaded from http:// sourceforge.net/ and implemented within CoGe under the title SynMap.”
Comparative Genomics (2007, neutral): “-> (4 7 [6 5] 9 10 11 12 13 14 15 16 18 17 19 20 [8] 1 2 3)”
A reference genome for common bean and genome-wide analysis of dual domestications (2014, neutral): “Synteny blocks within and between Glycine and Phaseolus were identified by first making blast comparisons of peptide sequences, followed by filtering to top hits per chromosome pair, and then synteny prediction with DAGchainer (Haas et al. 2004).”
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity (2012, methodology): “This class of methods has been implemented in software tools such as DAGchainer (17), ColinearScan (18), MCScan (19), SyMAP (20), FISH (21) and CYNTENATOR (22).”
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. (2008, methodology): “A pairwise alignment procedure was implemented using an empirical scoring scheme similar to that of Haas et al. (2004). The default scoring scheme (configurable) is min(log10 E, 50) match score for one gene pair, and 1 gap penalty for each 10-kb distance between any two consecutive gene pairs.”