Table 2 Computational techniques for in silico aptamer development
Bioinformatic tool | System requirements | Description and features | Refs. |
|---|---|---|---|
Aptamotif | Linux/Mac OS | Aptamotif is a computational method for the identification of sequence–structure RNA binding motifs in SELEX-derived aptamers | [35] |
Galaxy | Web/Linux/Mac OS | Analysis of pre-processing and analyzing HTS-SELEX sequencing data using the Galaxy platform outcomes candidate aptamer sequences | |
AptCompare | Linux/Mac OS/Windows/Galaxy | AptCompare is an automated tool designed for pre-processing and analyzing HTS-SELEX sequencing data. The tool evaluates the performance of six commonly used aptamer motif discovery programs and utilizes a meta-rank metric to identify the most promising aptamer targets | [38] |
PATTERNITY.seq© | Linux/Mac OS/Windows | PATTERNITY-Seq© manages millions of sequences from raw sequencing datas to identify better aptamers in a faster way, (this tool regroups sequences in families, monitors the evolution of each family and each individual sequence, identifies enriched structure motifs, and studies the effect of selection pressure) | [39] |
MEME/GLAM | Linux/Mac OS/Web | To design aptasensors by identifying motifs in aptamers through MEME analysis | [40] |
MP Bind | Linux/Mac OS | MP Bind is a meta-motif-based statistical framework for predicting aptamers that bind to targets from SELEX-Seq data and proficiently managing biases caused by incomplete sequencing of aptamer pools or PCR | [41] |
APTANI | Linux/Mac OS | APTANI is a computational tool to select aptamers through sequence-structure motif analysis of HT-SELEX data | [42] |
APTANI2 | Linux/Mac OS | APTANI2 is an expanded and optimized version of APTANI. This tool includes modules for investigating sequence motifs and secondary structures, as well as a user-friendly graphical interface and coding solutions that improve performance | [43] |
AptCompare | Linux/Mac OS/Windows | AptCompare is a program that combines six analytical approaches for identifying RNA aptamer motifs across platforms | [38] |
COMPAS (COMmon PAtternS) | Unknown | COMPAS (COMmon PAtternS) is a program that was developed to support the entire SELEX process can find motif combinations | [44] |
RaptRankerr | Linux/Mac OS | RaptRanker as an RNA aptamer selection tool analyzes HT-SELEX data by evaluating the nucleotide sequence and secondary structure | [45] |
FASTAptamer | Linux/Mac OS/Windows | FASTAptamer performs the simple tasks of counting, comparing sequences, clustering sequences, calculating fold enrichment, and searching degenerately for nucleotide sequence motifs | [46] |
FASTAptameR | Web tool | FASTAptameR is an expanded set of interconnected modules such as Count, Distance, Cluster, Mutation network, Motif Discovery modules that can be used to interactively analyze and visualize HTS data | [47] |
SMART-Aptamer | Mac OS/Windows | Based on multilevel structure analysis, SMART-Aptamer identifies high-affinity aptamers with low false positive and negative rates from HTS data of SELEX libraries | [48] |
FSBC | Linux/Mac OS/Windows | FSBC estimates clusters considering different lengths of over-represented strings as target binding regions for HT-SELEX data | [49] |
AptaPLEX | Linux/Mac OS/Windows | AptaPLEX is a utility designed specifically for demultiplexing raw HT-SELEX data into corresponding selection cycles based on barcode information | [34] |
AptaSIM | Linux/Mac OS/Windows | AptaSim aimed at realistically recreating the selection process during SELEX using error-prone PCR | [50] |
AptaMUT | Linux/Mac OS/Windows | A new technique has been developed to identify polymerase errors that result in improved binding affinity compared to the original sequence | [50] |
AptaCLUSTER | Linux/Mac OS/Windows | AptaCluster allows for an efficient clustering of whole HT-SELEX aptamer pools | [51] |
AptaTRACE | Linux/Mac OS/Windows | AptaTRACE consists of three components: data preprocessing, secondary structure profile prediction, and motif extraction. These three components are controlled through a single configuration file | [52] |
AptaGUI | Linux/Mac OS/Windows | AptaGUI is a valuable resource that facilitates the implementation of the AptaTools package. This program allows for visual inspection of HT-SELEX experiments in a concise and efficient manner | [53] |
AptaTools package | Linux/Mac OS/Windows | This package encompasses several algorithms, such as AptaMUT, AptaCLUSTER and AptaGUI, that are instrumental in analyzing HT-SELEX data. These algorithms enable the identification of any possible flaws in the selection protocol, the discovery of aptamer candidates, and the provision of comprehensive sequence and structure-based analysis | [53] |
AptaSUITE | Linux/Mac OS/Windows | AptaSUITE incorporates a set of previously published algorithms, namely AptaPLEX, AptaSIM, AptaCLUSTER, and AptaTRACE | [54] |