HT-SELEX data analysis bioinformatics software tools
High-Throughput (HT) SELEX combines SELEX (Systematic Evolution of Ligands by EXponential Enrichment), a method for aptamer discovery, with massively parallel sequencing technologies. This emerging technology provides data for a global analysis of the selection process and for…
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HTPSELEX
Data

HTPSELEX

A database containing sets of in vitro selected transcription factor (TF)…

A database containing sets of in vitro selected transcription factor (TF) binding site sequences obtained with systematic evolution of ligands by exponential enrichment (SELEX) method. HTPSELEX…

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MPBind
Desktop

MPBind

A meta-motif based statistical framework and pipeline to predict SELEX derived…

A meta-motif based statistical framework and pipeline to predict SELEX derived binding aptamers. Briefly, MPBind calculates four kinds of p-values (1-sided) for each motif, representing different…

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ValFold
Desktop

ValFold

A program for the aptamer truncation process. ValFold can predict the secondary…

A program for the aptamer truncation process. ValFold can predict the secondary structures with improved accuracy based on unique aptamer characteristics. ValFold predicts not only the canonical…

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AptaTRACE
Desktop

AptaTRACE

An approach for the identification of sequence-structure binding motifs in…

An approach for the identification of sequence-structure binding motifs in HT-SELEX derived aptamers. AptaTRACE leverages the experimental design of the SELEX protocol and identifies…

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FASTAptamer
Desktop
Web

FASTAptamer

An easy-to-use and universally compatible toolkit designed for bench scientists…

An easy-to-use and universally compatible toolkit designed for bench scientists to address the primary sequence analysis needs from high-throughput sequencing of combinatorial selection populations.…

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APTANI
Desktop

APTANI

A computational tool to identify target-specific aptamers from HT-SELEX data…

A computational tool to identify target-specific aptamers from HT-SELEX data and secondary structure information. APTANI builds on AptaMotif algorithm (Hoinka et al., 2012), originally implemented to…

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HTS-IBIS
Desktop

HTS-IBIS HTS Inference of BInding Sites

Corrects for technological biases, selects the cycle and k, and builds a motif…

Corrects for technological biases, selects the cycle and k, and builds a motif starting from a consensus k-mer in that cycle. In large scale tests, HTS-IBIS outperformed the extant automatic…

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AptaTools
Desktop

AptaTools

Provides a complete and comprehensive analysis pipeline for HT-SELEX data and…

Provides a complete and comprehensive analysis pipeline for HT-SELEX data and comprises four fully automated core steps: data preprocessing, sequence analysis, cluster extraction, and data…

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FastMotif
Desktop

FastMotif

A motif discovery algorithm that is built on a recent machine learning…

A motif discovery algorithm that is built on a recent machine learning technique referred to as Method of Moments. Based on spectral decompositions, this method is robust to model misspecifications…

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Aptamer Base
Data

Aptamer Base

Provides structured and detailed information about the experimental conditions…

Provides structured and detailed information about the experimental conditions under which aptamers were selected and their binding affinity quantified. Aptamer Base is an open collaborative database…

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Aptaligner
Desktop

Aptaligner

Aligns pseudorandom DNA X-aptamers from next-generation sequencing data.…

Aligns pseudorandom DNA X-aptamers from next-generation sequencing data. Aptaligner uses the inherent design scheme of bead-based X-aptamers to create a hypothetical reference library and Markov…

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