The Department of NanoMedicine and BioMedical Engineering



Aptaligner© a is GUI-driven software package for the analysis of next-generation sequencing data contained in a FASTQ file. The software is designed to handle the pseudo-random aptamer sequences inherent in X-Aptamers, but it can also handle more typical aptamer and DNA sequences with defined primers and/or tags as well. Users are highly encouraged to use version 2.1, which is a GUI-driven package with sequence length cut-off and noise level filters that is ~100 times faster than the original command line driven version 1.0. 

Having troubles? Check out our FAQ page.

The Aptaligner v2.1 User Guide contains step-by-step instructions for both installation and usage.

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A linux-based operating system is required, and while at least 4 nodes is recommended, it can be run using only 1 CPU. To date the software has been tested on a laptop, a small server with 8 CPUs (cores), and a larger server with 54 CPUs (cores). The software has been tested using RedHat 6.5 and Fedora 20 with success. Significant free disk space (up to 12 GB) and RAM (1 to 4 GB) may be required, depending on the complexity and number of library design files, the size of the FastQ file, and the run-time options chosen for length and noise cut-off values. Memory as low as 0.25 GB has worked successfully. Much of the code is parellelized for faster run times. It is coded to use 50% of the available total memory.


R Software Package with modules  MiscPsycho,  statmod,  stringr,   and dendroextras

Python including xlrd, argparse and openpyxl, Biopythonnumpy and C.


Latest Version

Aptaligner© v2.1 source code only (1 MB) Added length error and noise level filters

Aptaligner© v2.1 (580 MB) Including FastQ example files and output data

Previous Versions

Aptaligner© v2.0 source code (4 MB) Added a GUI interface and improved speed

Aptaligner© v1.1 source code (4 MB) minor bug fixes

Aptaligner© v1.0 source code (4 MB)



Latest Version (2.1) (2.6 MB) (FastQ file not included - see Example Input) (9.4 MB) (FastQ file not included - see Example Input)

Previous Versions (2.0 and 1.1)

Short_test_output (16 MB)

Medium_test_output (16 MB)

Short_test_output (16 MB)

Medium_test_output (138 MB)

Long_test_output (1359 MB)


When citing the Aptaligner© software package, please cite the following publication:

Emily Lu, Miguel-Angel Elizondo-Riojas, Jeffrey T. Chang and David E. Volk, "Aptaligner: Automated Software for Aligning Pseudo-Random DNA X-Aptamers from Next-Generation Sequencing Data", Biochemistry 53(22), 3523-3525, May 27, 2014. DOI:10.1021/bi500443e


The development of Aptaligner© was financially supported by The Center for Clinical and Translational Sciences (NIH/NCRR UL1 TR000371), the NCI (CA15668), The Welch Foundation(AU-1296), the NIAID (HHSN2772200800048C) and the NHLBI(HHSN268201000037C).

This copyrighted Aptaligner© software package is freely available to all non-commercial users. Although users are encouraged to modify the code to meet their specific needs, the copyright of any such modified code is retained by the Regeants of The University of Texas System.

This page was last modified by on August 18, 2014.