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Related Concept Videos

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Related Experiment Video

Updated: Jun 9, 2026

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
06:40

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Published on: March 22, 2018

GASSST: global alignment short sequence search tool.

Guillaume Rizk1, Dominique Lavenier

  • 1Univ-Rennes 1/IRISA, IRISA - Symbiose Campus universitaire de Beaulieu, 35042 Rennes Cedex, France. guillaume.rizk@irisa.fr

Bioinformatics (Oxford, England)
|August 27, 2010
PubMed
Summary
This summary is machine-generated.

A new aligner, GASSST (Global Alignment Short Sequence Search Tool), offers fast and sensitive DNA sequence alignment without restricting indels, even for long reads. It outperforms existing tools in speed and accuracy for next-generation sequencing data.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Next-generation sequencing generates vast amounts of data, necessitating fast and accurate alignment software.
  • Current aligners face challenges with speed, indel flexibility, and efficiency on increasingly large sequence reads.

Purpose of the Study:

  • To develop a novel aligner, GASSST (Global Alignment Short Sequence Search Tool), that achieves high performance without indel restrictions.
  • To ensure the aligner remains effective for long reads generated by modern sequencing technologies.

Main Methods:

  • Implemented an efficient filtering step to rapidly discard suboptimal alignments before dynamic programming.
  • Utilized a precomputed table of alignment scores for short sequences and a novel approximation algorithm.
  • Compared GASSST performance against established aligners: BWA, BFAST, SSAHA2, and PASS.

Main Results:

  • GASSST demonstrates high sensitivity across various configurations.
  • Achieved faster overall execution times compared to state-of-the-art aligners.
  • Effectively handles long reads without compromising speed or accuracy.

Conclusions:

  • GASSST provides a significant advancement in DNA sequence alignment tools.
  • Offers a balance of speed, sensitivity, and flexibility for large-scale genomic applications.
  • Represents an efficient solution for analyzing data from next-generation sequencing technologies.