DAGchainer pipeline

DAGchainer specifications

Information


Unique identifier OMICS_11725
Name DAGchainer
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data DAGchainer requires a single tab-delimited input file which describes genes paired by BLAST matches and the E-value for each match.
Operating system Unix/Linux
Programming languages C++, Perl
License Artistic License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Brian Haas <>

Publication for DAGchainer

DAGchainer IN pipelines

 (9)
2016
PMCID: 4726258
PMID: 26786968
DOI: 10.1038/srep19427

[…] genes between artichoke and lettuce were identified using synmap77 on the coge platform (http://genomevolution.org) using last aligner (c-score filter = 0.4) and retrieving syntenic blocks with dagchainer adopting the following parameters: -d 10 -a 3 -dm 20. synonymous substitution densities (ks) among and between different genomes distribution were calculated over syntenic genes, […]

2015
PMCID: 4404975
PMID: 25954293
DOI: 10.3389/fpls.2015.00268

[…] located in large conserved blocks of m. truncatula, l. japonicus, c. arietinum, g. max, p. vulgaris, and c. cajan genomes. sequences were compared by the last (http://last.cbrc.jp/) algorithm. the dagchainer algorithm was used to identify syntenic regions between genomes. the search was based on relative gene order, with the maximum distance between two matches set to 20 genes and the minimum […]

2013
PMCID: 3878754
PMID: 24330712
DOI: 10.1186/1471-2229-13-212

[…] (evalue = 10-3) was used to identify homologous protein-coding and pre-mirna genes between foxtail millet and sorghum. (the sorghum pre-mirna sequences were downloaded from mirbase release 20) dagchainer [96] was used to identify collinear chains among the homologs. we used circos plots [97] to show the collinear relationships between the foxtail millet and sorghum pre-mirna sequences., […]

2012
PMCID: 3433357
PMID: 22769602
DOI: 10.1186/1471-2180-12-135

[…] order of e. faecium compared to its close relative e. faecalis, a blastp alignment of all the predicted proteins from the tx16 and v583 genomes was performed followed by orf synteny analysis using dagchainer [39]. the result showed that e. faecium tx16 gene order is very different from that of e. faecalis strain v583 (and therefore og1rf, which has a very similar synteny to v583 [40,41]) […]

2012
PMCID: 3445971
PMID: 22951933
DOI: 10.1128/mBio.00259-12

[…] for the construction of the maximal likelihood tree with the jones-taylor-thornton (jtt) model of the amino acid substitution. we manually inspected the gene order of clusters with the results from dagchainer (61). we considered a difference of 40% in the number of accessory genes to be significantly different., the sets of eukaryotic protein kinases (kinomes) of the seven dermatophyte species […]

DAGchainer institution(s)
The Institute for Genomic Research, Chinakville, MD, USA
DAGchainer funding source(s)
The Institute for Genomic Research, Rockville, MD, USA

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