DAGchainer statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool DAGchainer

Tool usage distribution map

This map represents all the scientific publications referring to DAGchainer per scientific context
info info

Associated diseases

This word cloud represents DAGchainer usage per disease context

Popular tool citations

chevron_left Synteny block detection chevron_right
Want to access the full stats & trends on this tool?


DAGchainer specifications


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




No version available


  • person_outline Brian Haas

Publication for DAGchainer

DAGchainer citations


A tutorial of diverse genome analysis tools found in the CoGe web platform using Plasmodium spp. as a model

PMCID: 5887277
DOI: 10.1093/database/bay030

[…] nMap (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 for […]


Inferring synteny between genome assemblies: a systematic evaluation

BMC Bioinformatics
PMCID: 5791376
PMID: 29382321
DOI: 10.1186/s12859-018-2026-4

[…] ny should be close to 100%, with the exception of default setting in Satsuma. All of the anchor-based programs use gene orthology to find anchor points during process of synteny blocks detection. For DAGchainer, i-ADHoRe and MCScanX, we obtained gene orthology from OrthoFinder [] (v0.2.8). SynChro has an implemented program called OPSCAN to scan for gene orthology. We arranged the following parame […]


Draft Genome Sequence and Annotation of the Apicomplexan Parasite Besnoitia besnoiti

Genome Announc
PMCID: 5690326
PMID: 29146849
DOI: 10.1128/genomeA.01200-17
call_split See protocol

[…] s, 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 on t […]


Global analysis of the MATE gene family of metabolite transporters in tomato

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

[…] shold 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 […]


Comparative analysis of genome sequences of the conifer tree pathogen, Heterobasidion annosum s.s.

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

[…] efined 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. […]


Echinochloa crus galli genome analysis provides insight into its adaptation and invasiveness as a weed

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

[…] with 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 grass s […]

Want to access the full list of citations?
DAGchainer institution(s)
The Institute for Genomic Research, Chinakville, MD, USA
DAGchainer funding source(s)
The Institute for Genomic Research, Rockville, MD, USA

DAGchainer reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review DAGchainer