DAGchainer protocols

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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

 (14)
2017
PMCID: 5604175
PMID: 28927400
DOI: 10.1186/s12915-017-0419-x

[…] were constructed based on the concatenated alignments of 2381 orthologous protein-coding genes using raxml 8.2.8 [] with a jtt + γ model and 1000 bootstraps., synmap [] using blastz [] alignments, dagchainer [] (options -d 30 and -a 2), and no merging of syntenic blocks were used as part of the coge platform [] to identify syntenic blocks between the hard-masked pseudo-chromosomes of d. […]

2016
PMCID: 4726258
PMID: 26786968
DOI: 10.1038/srep19427

[…] genes between artichoke and lettuce were identified using synmap 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 […]

2015
PMCID: 4663468
PMID: 26616172
DOI: 10.1038/srep17583

[…] segmentally duplicated chromosome blocks. sequence regions franking 50 kb upstream and downstream of targeted genes were submitted to the identification of segmentally duplicated blocks by using the dagchainer program. a minimum of 5 gene pairs was used to define a block., to survey the contribution of retrotransposons and dna transposons to the expansion of the susy, sps, spp and udpgp gene […]

2014
PMCID: 4079696
PMID: 24988301
DOI: 10.1371/journal.pone.0101136

[…] cs6. duplications in the foxtail millet genome and synteny between foxtail millet and rice were established utilizing the synmap tool (detailed settings are as following: blast algorithm: last, dagchainer options and merge syntenic blocks use the recommended parameters, and the synonymous (ks) and non-synonymous (ka) substitution rates were calculated using the codeml program ) […]


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DAGchainer in publications

 (65)
PMCID: 5887277
DOI: 10.1093/database/bay030

[…] (i) identifies putative syntenic gene pairs using a sequence comparison algorithm (last by default), (ii) identifies and filters tandem duplicated using a program called blast2raw and (iii) uses dagchainer to find collinear series of homologous genes or sequences and identify syntenic pairs. synmap uses codeml () to calculate the non-synonymous (kn) and synonymous (ks) substitution rates […]

PMCID: 5690326
PMID: 29146849
DOI: 10.1128/genomeA.01200-17

[…] with a higher weight assigned to genewise mappings., product names were assigned to protein coding genes in three steps. first, syntenic blocks between b. besnoiti and t. gondii were identified with dagchainer (), and b. besnoiti syntenic genes were assigned the product names from their t. gondii orthologues, as annotated in toxodb v34 (). next, b. besnoiti nonsyntenic genes were named based […]

PMCID: 5663081
PMID: 29084510
DOI: 10.1186/s12870-017-1115-2

[…] e-value ≤10e-4) were determined using blast2raw script in the coge toolkit. syntenic blocks (microsynteny within a genome or synteny between two genomes) were identified with synmap thorugh the dagchainer algorithm using the relative gene order option with a minimum of 5 gene pairs aligned and a maximum distance of 20 genes between two matches. quotaalign was used to merge adjacent syntenic […]

PMCID: 5654758
PMID: 29085779
DOI: 10.1016/j.gdata.2017.10.003

[…] by using blastp . protein sequences in h. annosum were used as query and searched against those in h. irregulare, followed by filtering the best hits. syntenic regions were identified by using dagchainer with default settings, and the micro-syntenic differences were shown with the selected regions., previously published pipelines were used in identification of putative genes encoding […]

PMCID: 5647321
PMID: 29044108
DOI: 10.1038/s41467-017-01067-5

[…] figtree. for genomic synteny, we first used blastp (e-value ≤ 10-7) to align the e. crus-galli protein dataset to that of s. bicolor, s. italica and itself. the alignments were then subjected to dagchainer to determine syntenic blocks. the 4dtv of each syntenic block was calculated by an in-house perl script., to build phylogenetic trees for the genes of momilactone a gene clusters, ten […]


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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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