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	[36, 37]
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]