AptaTRACE specifications

Information


Unique identifier OMICS_11497
Name AptaTRACE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data AptaTRACE takes as input the sequencing results from all, or a subset of selection cycles from an HT-SELEX experiment.
Output data It outputs a list of position specific weight matrices (PWMs) along with a visual representation of the motifs structural context shift throughout the selection.
Operating system Unix/Linux
Programming languages C++, Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Pawel F. Przytycki <>

Publication for AptaTRACE

AptaTRACE in publications

 (2)
PMCID: 5751119
PMID: 29186809
DOI: 10.3390/ijms18122516

[…] of mfold can analyze hundreds of sequences at once, it is, however, difficult to handle structure prediction on the hts scale. , a recently developed platform for structure motif clustering is aptatrace []. based on the secondary structure prediction from sfold [,], aptatrace applies this information into all of the sequences input to the program. this allows for the prediction […]

PMCID: 5198051
PMID: 27973417
DOI: 10.3390/ph9040076

[…] only 2.9% of the pool. this new structure was impossible to detect with low throughput sequencing but, interestingly, it demonstrated a strongest inhibition of the reverse transcriptase., “aptatrace” is another software that has been recently developed to identify structure motifs that are enriched during the selex []. using sfold [], predicted secondary structures are built […]


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AptaTRACE institution(s)
National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda MD, USA; Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, CA, USA; Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany

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