APTANI: A computational tool to select aptamers through sequence-structure motif analysis of HT-SELEX data

J. Caroli, C. Taccioli, A. De La Fuente, Paolo Serafini, S. Bicciato

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

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: Supplementary information: Supplementary data are available at Bioinformatics online.

Original languageEnglish (US)
Pages (from-to)161-164
Number of pages4
JournalBioinformatics
Volume32
Issue number2
DOIs
StatePublished - Jul 22 2015

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Epitopes
Nucleic acids
Bioinformatics
Nucleic Acids
SELEX Aptamer Technique
Ligands
Throughput
Availability
Molecules
Target
Computational Biology
Computational Analysis
Random Sequence
Graphical Representation
Secondary Structure
Sequencing
High Throughput
Affine transformation
Data Structures
Contact

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability

Cite this

APTANI : A computational tool to select aptamers through sequence-structure motif analysis of HT-SELEX data. / Caroli, J.; Taccioli, C.; De La Fuente, A.; Serafini, Paolo; Bicciato, S.

In: Bioinformatics, Vol. 32, No. 2, 22.07.2015, p. 161-164.

Research output: Contribution to journalArticle

Caroli, J. ; Taccioli, C. ; De La Fuente, A. ; Serafini, Paolo ; Bicciato, S. / APTANI : A computational tool to select aptamers through sequence-structure motif analysis of HT-SELEX data. In: Bioinformatics. 2015 ; Vol. 32, No. 2. pp. 161-164.
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