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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
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Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
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PASS: a program to align short sequences.

Davide Campagna1, Alessandro Albiero, Alessandra Bilardi

  • 1CRIBI Biotechnology Centre, University of Padua, Padova, Italy.

Bioinformatics (Oxford, England)
|February 17, 2009
PubMed
Summary
This summary is machine-generated.

New DNA sequencing technologies generate vast data, overwhelming standard alignment tools. The developed program, PASS, offers significantly faster and more sensitive DNA sequence alignment for handling large datasets.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Next-generation sequencing (NGS) technologies produce massive amounts of DNA sequence data.
  • Existing DNA alignment programs struggle to efficiently process this large-scale data.

Purpose of the Study:

  • To develop a novel DNA alignment program, PASS, addressing the limitations of current tools for NGS data.
  • To enhance both execution speed and sensitivity in aligning short DNA sequences to a reference genome.

Main Methods:

  • PASS utilizes a seed-and-extend algorithm with precomputed scores for short words.
  • It employs an in-memory index of genomic positions for 'seed' words and alignment scores.
  • The process involves finding seed matches, checking flanking regions, and performing dynamic alignment.

Main Results:

  • PASS demonstrates superior performance in both speed and sensitivity compared to existing programs like BLAST and SOAP.
  • Gap alignment is notably faster, achieving hundreds of times the speed of BLAST.
  • The program effectively handles large volumes of short DNA reads from platforms like Solexa, SOLiD, and 454.

Conclusions:

  • PASS is a highly effective tool for aligning short DNA sequences to reference genomes, particularly for NGS data.
  • Its speed and sensitivity offer a significant improvement over standard alignment methods.
  • The program is freely available for Linux and Windows.