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ArchTEx specifications


Unique identifier OMICS_08559
Name ArchTEx
Alternative name Architectural Tag Extender
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequence data
Input format BAM
Output data ArchTEx graphically displays the cross-correlation plot showing the peaks of predicted DNA length.
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Michael J. Buck

Publication for Architectural Tag Extender

ArchTEx citations


Genome Wide Identification of Target Genes for the Key B Cell Transcription Factor Ets1

Front Immunol
PMCID: 5383717
PMID: 28439269
DOI: 10.3389/fimmu.2017.00383
call_split See protocol

[…] on the Ets1 consensus motif. ChIP-seq data for acetylated and methylated lysine variants of histone H3 in primary B cells were obtained from the GEO database and are reported in Ref. (–). The program ArchTex () was then used to map average histone modifications surrounding the Ets1 consensus-binding sites. As a control, ArchTex was also used to align histone modifications surrounding 60,000 random […]


Chromatin Mediation of a Transcriptional Memory Effect in Yeast

PMCID: 4426369
PMID: 25748434
DOI: 10.1534/g3.115.017418

[…] scriptionally responsive genes were generated using data for 69 transcriptionally responsive targets and 64 memory effect targets () containing unique Abf1 sites. ChIP-seq data were analyzed with the ArchTEx program () and Z-scored to normalize for variance between experiments after calculating the log2 ratio. To obtain Z-scores, sequence tags were first extended to a total length of 120 bp to acc […]


Chromatin accessibility: a window into the genome

PMCID: 4253006
PMID: 25473421
DOI: 10.1186/1756-8935-7-33

[…] he experiment was successful and is often performed by constructing composite plots and by visualization (Steps 4, 6, 9, and 12). Multiple tools are available for generating composite plots including ArchTEX [], DANPOS-profile [], and CEAS []. For example, TSSs have been shown to be chromatin accessible on average across all eukaryotic genomes [, , ]. A drop of composite plot signal intensity is e […]


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ArchTEx institution(s)
Department of Biochemistry, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY, USA; Molecular Epidemiology and Functional Genomics, Roswell Park Cancer Institute, Buffalo, NY, USA
ArchTEx funding source(s)
National Science Foundation (grant IIS1016929)

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