Aptamer discovery is a complex process. Following library enrichment against the desired target, the best aptamer candidates are identified from millions of potential sequences. Whether you are new to aptamer selection or simply short on manpower, Base Pair is here to help.
Following next generation sequencing, up to 10 million sequences are evaluated using proprietary bioinformatics techniques. A FASTQ file containing sequence information from final aptamer pools or pools from several selection rounds is uploaded to a secure ftp site.
Sufficient enrichment is first confirmed. Then the top 20 candidates are identified based on sequence length, frequency count, predicted stability (Gibb’s free energy), and sequence motifs. Sequence information and predicted structures are provided in a detailed bioinformatics report.
A Venn diagram is generated for analysis involving multiple pools that have been barcoded. The diagram indicates overlapping sequences between selection rounds.
This technique can also be applied to identify individual- and pan-binders to multiple targets as part of Base Pair’s patented multiplex selection.
Contact Base Pair to learn more.