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APTANI2: update of aptamer selection through sequence-structure analysis

2019; Oxford University Press; Volume: 36; Issue: 7 Linguagem: Inglês

10.1093/bioinformatics/btz897

1367-4811

Jimmy Caroli, Mattia Forcato, Silvio Bicciato,

Machine Learning in Bioinformatics

Here we present APTANI2, an expanded and optimized version of APTANI, a computational tool for selecting target-specific aptamers from high-throughput-Systematic Evolution of Ligands by Exponential Enrichment data through sequence-structure analysis. As compared to its original implementation, APTANI2 ranks aptamers and identifies relevant structural motifs through the calculation of a score that combines frequency and structural stability of each secondary structure predicted in any aptamer sequence. In addition, APTANI2 comprises modules for a deeper investigation of sequence motifs and secondary structures, a graphical user interface that enhances its usability, and coding solutions that improve performances.Source code, documentation and example command lines can be downloaded from http://aptani.unimore.it. APTANI2 is implemented in Python 3.4, released under the GNU GPL3.0 License, and compatible with Linux, Mac OS and the MS Windows subsystem for Linux.Supplementary information is available at Bioinformatics online.