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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…
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BEEMEL
Desktop

BEEMEL Binding Energy Estimates using Maximum Likelihood

Selects the optimal motif length and calculates the confidence intervals of…

Selects the optimal motif length and calculates the confidence intervals of estimated parameters. BEESEL uses the expectation maximization (EM) algorithm to iteratively find both the optimal position…

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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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HTPSELEX
Dataset

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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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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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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hts-exploration
Desktop

hts-exploration

Analyzes in vitro selection data for RNA-protein interactions that may…

Analyzes in vitro selection data for RNA-protein interactions that may primarily rely on specific local features in the context of a larger secondary structure. hts-exploration is a Clojure library…

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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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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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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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SELEX
Desktop

SELEX

Functions to assist in discovering transcription factor DNA binding…

Functions to assist in discovering transcription factor DNA binding specificities from SELEX-seq experimental data. SELEX is an R package that offers functions used to calculate and return the…

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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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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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Aptamer Base
Dataset

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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