FrameWorker specifications

Information


Unique identifier OMICS_26746
Name FrameWorker
Interface Web user interface
Restrictions to use License purchase required
Input data A set of DNA sequences.
Input format EMBL,FASTA,GCG,RSF,GenBank,IG
Output data A model overview, graphical view of the models and the common elements, model details and common elements.
Computer skills Basic
Stability Stable
Free trial Yes
Registration required Yes
Maintained Yes

Maintainer


  • person_outline GGA Team <>

Additional information


FrameWorker is part of GEMS Launcher, which is part of Genomatix Software Suite. http://www.genomatix.de/online_help/help_gems/FrameWorker.html

FrameWorker in publications

 (26)
PMCID: 5773596
PMID: 29348434
DOI: 10.1038/s41467-017-01995-2

[…] actually present in at least three promoters of each set. each promoter set was analyzed separately for the presence of more cassettes shared by at least three promoters per set using the program frameworker (genomatix, munich). parameters were set according to the supplier’s defaults, except for sequence quorum which was adapted top-down until more cassettes were found. the distance range […]

PMCID: 5746105
PMID: 29296203
DOI: 10.18632/oncotarget.21201

[…] positional weight matrices available within the matinspector database of the genomatix software suite (-). the co-occupancy of different tfbs at gene specific promoters was also analysed with the frameworker tool that encompasses the vertebrate matrix library 9.2 of the matinspector database. among enriched tfbs we found two significant modules with two elements in liver specific gene […]

PMCID: 4671726
PMID: 26641263
DOI: 10.1371/journal.pone.0144158

[…] (lg4:20865175–20889027), npas2 (lg14:11922193–11945535) and gnrh2 (lg1a:10673952–10675997)., promoter sequences were compared by definition of a similar pattern or framework of tfbss (software frameworker, genomatix, www.genomatix.de) following a previously described methodology [–]. a framework is defined as a set of two or more tfbss with a specific order, strand orientation, […]

PMCID: 4236145
PMID: 25405900
DOI: 10.1371/journal.pone.0113215

[…] +100 bps) of human, mouse, rat, cow and dog were taken from ensembl. sequences were aligned and analyzed for phylogenetic conserved transcription factor binding sites (tfbs) using matinspector and frameworker programs from genomatix software suite., mice were anesthetized by using isoflurane gas (aerrane; baxter, lessines, belgium). peripheral blood samples were obtained from the retro-orbital […]

PMCID: 3897978
PMID: 24418414
DOI: 10.1186/1471-2407-14-16

[…] sequences 3,000 bp homologue segments were evaluated allowing 500 bp overlap of segments at each composite model scanning step. dna sequence segments of all examined species were analyzed by the frameworker (version 5.4.3.3, http://www.genomatix.de) for conserved composite model matches by using the matrix family library 7.1 at the following settings: core promoter elements 0.75/optimized, […]


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