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HT-SELEX software tools

High-throughput sequencing 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 simultaneous discovery of a large number of candidates but currently lacks dedicated computational approaches for their analysis. Source text: Hoinka et al., 2015.

APTANI

OMIC_10073

APTANI

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

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 analyze SELEX data; extends the applicability of…

AptaTools

OMIC_09204

AptaTools

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

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 visualization. At the same time, AptaTools is modular enough…

AptaTRACE

OMIC_11497

AptaTRACE

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

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 sequence-structure motifs that show a signature of selection.…

FASTAptamer

OMIC_10074

FASTAptamer

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

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. FASTAptamer performs the simple tasks of counting,…

FastMotif

OMIC_08473

FastMotif

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

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 and is not prone to locally optimal solutions.

HTS Inference of BInding Sites

OMIC_09477

HTS Inference of BInding Sites
HTS-IBIS

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

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 algorithm for the motif finding task on both in vitro and…

MPBind

OMIC_09205

MPBind

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

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 features. Using human embryonic stem cell SELEX-Seq…