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Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....

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Related Experiment Video

Updated: Apr 29, 2026

In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses

In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses

Published on: September 7, 2022

Aptaligner: automated software for aligning pseudorandom DNA X-aptamers from next-generation sequencing data.

Emily Lu¹, Miguel-Angel Elizondo-Riojas, Jeffrey T Chang

¹UTHealth Bioinformatics Service Center, ‡Center for Clinical and Translational Sciences, §School of Biomedical Informatics, ∥Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, ⊥Department of Nanomedicine and Biomedical Engineering, @School of Medicine, and #Department of Integrated Biology and Pharmacology, University of Texas Health Science Center , 6431 Fannin Street, Houston, Texas 77030, United States.

|May 29, 2014

Summary

New software, Aptaligner, improves DNA/RNA sequence alignment for specialized X-aptamers. It uses a novel approach to handle complex bases, enhancing next-generation sequencing analysis for aptamer discovery.

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Collection and Extraction of Saliva DNA for Next Generation Sequencing

Collection and Extraction of Saliva DNA for Next Generation Sequencing

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Collection and Extraction of Saliva DNA for Next Generation Sequencing

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Published on: August 27, 2014

Area of Science:

Biotechnology
Bioinformatics
Molecular Biology

Background:

Next-generation sequencing (NGS) of bead-based aptamer libraries faces challenges with traditional alignment software.
Specialty bases (W, X, Y, Z) in X-aptamers complicate accurate sequence alignment.

Purpose of the Study:

To develop an automated program for improved alignment of bead-based X-aptamer sequences.
To address the limitations of existing DNA/RNA alignment tools for complex aptamer libraries.

Main Methods:

Developed Aptaligner, an automated program utilizing the inherent design scheme of bead-based X-aptamers.
Implemented Markov modeling techniques for enhanced sequence alignment accuracy.
Incorporated features for length error and noise level cutoffs, parallel processing, and project sorting.

Main Results:

Aptaligner provides improved alignment for X-aptamers with specialty bases.
The software effectively handles the complexities introduced by special base encoding.
Parallelization enables efficient processing of large datasets from single chips.

Conclusions:

Aptaligner offers a significant advancement in analyzing NGS data from bead-based aptamer libraries.
The tool enhances the accuracy and efficiency of aptamer discovery and characterization.
This facilitates more robust research in fields utilizing aptamer technology.