Peer-Reviewed Journal Details
Mandatory Fields
Shieh, KR;Kratschmer, C;Maier, KE;Greally, JM;Levy, M;Golden, A
2020
May
Bioinformatics
AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX
Published
Optional Fields
36
2905
2906
aSummary: High-throughput sequencing can enhance the analysis of aptamer libraries generated by the Systematic Evolution of Ligands by EXponential enrichment. Robust analysis of the resulting sequenced rounds is best implemented by determining a ranked consensus of reads following the processing by multiple aptamer detection algorithms. While several such approaches have been developed to this end, their installation and implementation is problematic. We developed AptCompare, a cross-platform program that combines six of the most widely used analytical approaches for the identification of RNA aptamer motifs and uses a simple weighted ranking to order the candidate aptamers, all driven within the same GUI-enabled environment. We demonstrate AptCompare's performance by identifying the top-ranked candidate aptamers from a previously published selection experiment in our laboratory, with follow-up bench assays demonstrating good correspondence between the sequences' rankings and their binding affinities.
1367-4803
10.1093/bioinformatics/btaa054
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