General Information
| Description | A computational tool to select aptamers through sequence-structure motif analysis of HT-SELEX data |
| Homepage | http://aptani.unimore.it |
Publications
APTANI: a computational tool to select aptamers through sequence-structure motif analysis of HT-SELEX data
Motivation:
Aptamers are synthetic nucleic acid molecules that can bind biological targets in virtue of both their sequence and three-dimensional structure. Aptamers are selected using SELEX, Systematic Evolution of Ligands by EXponential enrichment, a technique that exploits aptamer-target binding affinity. The SELEX procedure, coupled with high-throughput sequencing (HT-SELEX), creates billions of random sequences capable of binding different epitopes on specific targets. Since this technique produces enormous amounts of data, computational analysis represents a critical step to screen and select the most biologically relevant sequences.
Results:
Here, we present APTANI, a computational tool to identify target-specific aptamers from HT-SELEX data and secondary structure information. APTANI builds on AptaMotif algorithm, originally implemented to analyze SELEX data; extends the applicability of AptaMotif to HT-SELEX data and introduces new functionalities, as the possibility to identify binding motifs, to cluster aptamer families or to compare output results from different HT-SELEX cycles. Tabular and graphical representations facilitate the downstream biological interpretation of results.
Availability and implementation:
APTANI is available at http://aptani.unimore.it.
Contact:
silvio.bicciato@unimore.it
Supplementary information:
Supplementary data are available at Bioinformatics online.
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