Aptamer Database
How did we collect and review the information?
Aptamer information is collected by a trained undergraduate researcher from The University of Texas Freshman Research Initiative (FRI) Aptamer Stream. This researcher, also called the information collector, extracts aptamer and selection information from a peer-reviewed publication and deposits that information into the research team’s Google Sheet. The following information is collected for each aptamer record.
A summary of current aptamer modifications in the UTexas Aptamer Database.
Aptagen Cross Referencing
A previous effort from our research group had demonstrated that there may be a high error rate for accurately reporting aptamer sequences (Miller et al., 2022). While this issue can only be addressed as a community by the establishment of standards in databases and publications, we attempted to monitor our own efforts at standardization and curation by incorporating and comparing aptamer sequence results from another aptamer database: Apta-Index (Aptagen company in Jacobus, PA). Apta-Index was originally chosen for two reasons: first, it is active as sequences are regularly added to the site; and second, it is sufficiently large for comparative purposes, containing almost 800 aptamer sequences (July 2023).
Previous and Current Aptamer Databases
| Database Name (link embedded) | Institution | Aptamer Sequences (as of April 2023) | Current Status | First launched or date of publication | Reference (link embedded) |
|---|---|---|---|---|---|
| SELEX_DB | Institute of Cytology and Genetics | 116 | Last updated 2015 | 2000 | Ponomarenko, et al., 2000 Ponomarenko, et al., 2002 |
| Aptamer Database* | The University of Texas at Austin | 239 | Inactive | 2004 | Lee, et al., 2004 |
| RiboaptDB* | University of Southern Mississippi | 3842 | Inactive | 2006 | Thodima, et al., 2006 |
| HTPSELEX | Swiss Institute for Experimental Cancer Research and Swiss Institute of Bioinformatics | Not determined | Last updated September 2012 | 2006 | Jagannathan, et al., 2006 |
| Apta-Index™ | Aptagen | 783 (as of April 2023) | Active and updated | 2008 | No paper to date. |
| Aptamer Base* | Carleton University | 2334 | Inactive (CSV file with aptamer sequence information is available on GitHub) | 2012 | Cruz-Toledo, et al., 2012 McKeague, el al., 2015 |
| Aptabase | Indian Institute of Technology Guwahati | 605 | Periodically updated | 2021 | No paper to date. |
| AptaDB | East China University of Science and Technology | 1350 | Not determined | 2023 | Chen, et al, 2023 |
