ArticleBioinformatics (Oxford, England)2020
AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed, 19 citations in OpenAlex.
- AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers.Molecular therapy. Nucleic acids · 2024Article
- Current developments of SELEX technologies and prospects in the aptamer selection with clinical applications.Journal, genetic engineering & biotechnology · 2024Review
- Aptamers as an approach to targeted cancer therapy.Cancer cell international · 2024Review
- AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers.bioRxiv : the preprint server for biology · 2023Article
- Design and Prediction of Aptamers Assisted by In Silico Methods.Biomedicines · 2023Review
- In vitro selection of aptamers and their applications.Nature reviews. Methods primers · 2023Article
- Target-switch SELEX: Screening with alternating targets to generate aptamers to conserved terminal dipeptides.STAR protocols · 2022Article
- FASTAptameR 2.0: A web tool for combinatorial sequence selections.Molecular therapy. Nucleic acids · 2022Article
- Electrochemical Aptasensors for Antibiotics Detection: Recent Achievements and Applications for Monitoring Food Safety.Sensors (Basel, Switzerland) · 2022Review
- Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology.International journal of molecular sciences · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
Abstract
summaryHigh-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. AVAILABILITY AND IMPLEMENTATION: The source code and pre-built virtual machine images are freely available at https://bitbucket.org/shiehk/aptcompare. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.