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…
G T A T C G C T A HTPSELEX HTPSELEX

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…

Desktop app
G T A T C G C T A MPBind MPBind

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…

Desktop app
G T A T C G C T A ValFold ValFold

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…

Desktop app
G T A T C G C T A AptaTRACE AptaTRACE

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…

Desktop app
Web app
G T A T C G C T A FASTAptamer FASTAptamer

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.…

Desktop app
G T A T C G C T A APTANI APTANI

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…

Desktop app
G T A T C G C T A HTS Inference of… HTS Inference of BInding Sites

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…

Desktop app
G T A T C G C T A AptaTools AptaTools

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…

Desktop app
G T A T C G C T A FastMotif FastMotif

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…

G T A T C G C T A Aptamer Base Deprecated Aptamer Base

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…

Desktop app
G T A T C G C T A Aptaligner Deprecated Aptaligner

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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