The Department of NanoMedicine and BioMedical Engineering

Aptaligner

Aptaligner©

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. 

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

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HARDWARE REQUIREMENTS

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.

OTHER SOFTWARE REQUIRED

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

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

SOURCE CODE

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)

EXAMPLE INPUT FILES

Short_test_input.zip (2.5 MB)

Medium_test_input.zip (24 MB)

Long_test_input.zip (347 MB)

EXAMPLE OUTPUT FILES

Latest Version (2.1)

Medium_test_output_v2.1.zip (2.6 MB) (FastQ file not included - see Example Input)

Long_test_output_v2.1.zip (9.4 MB) (FastQ file not included - see Example Input)

Previous Versions (2.0 and 1.1)

Short_test_output v2.0.zip (16 MB)

Medium_test_output v2.0.zip (16 MB)

Short_test_output v1.1.zip (16 MB)

Medium_test_output v1.1.zip (138 MB)

Long_test_output v1.1.zip (1359 MB)

CITATIONS FOR APTALIGNER©

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 May 27, 2014. DOI:10.1021/bi500443e

FUNDING SUPPORT

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 David.Volk@uth.tmc.edu on June 25, 2014.