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Spatial Temporal Analysis of Fieldwise Flow in Microvasculature
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Published on: November 18, 2019

FAAST: Flow-space Assisted Alignment Search Tool.

Fredrik Lysholm1, Björn Andersson, Bengt Persson

  • 1IFM Bioinformatics and SeRC (Swedish e-Science Research Centre), Linköping University, S-581 83 Linköping, Sweden. frely@ifm.liu.se

BMC Bioinformatics
|July 21, 2011
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Summary

This study introduces FAAST, a novel algorithm for 454 sequencing data alignment. FAAST utilizes flowpeak information to significantly improve alignment accuracy and speed for high throughput sequencing.

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Large-area Scanning Probe Nanolithography Facilitated by Automated Alignment and Its Application to Substrate Fabrication for Cell Culture Studies

Published on: June 12, 2018

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • High throughput pyrosequencing (454 sequencing) is a key platform for long-read data generation.
  • Pyrosequencing errors, primarily gaps, are challenging for conventional alignment programs, leading to inaccuracies.
  • Existing alignment tools struggle to effectively handle the unique error profiles of 454 sequencing data.

Purpose of the Study:

  • To develop a novel algorithm for optimal local alignment of pyrosequencing data.
  • To improve alignment accuracy by incorporating flowpeak information specific to 454 sequencing.
  • To create a computational tool that enhances the analysis of 454 sequencing reads.

Main Methods:

  • Developed a new algorithm leveraging flowpeak information from 454 sequencing SFF files.
  • Implemented the algorithm in a software tool named FAAST (Flow-space Assisted Alignment Search Tool).
  • Utilized simulations to evaluate the accuracy and performance of FAAST against established methods.

Main Results:

  • FAAST demonstrates improved alignment accuracy, gaining several percentage points over Smith-Waterman-Gotoh.
  • Accuracy gains are dependent on the quality of the 454 sequencing data.
  • The FAAST program offers high-speed alignment due to its efficient multi-thread aware implementation.

Conclusions:

  • FAAST provides a significant improvement in alignment accuracy for 454 sequencing data.
  • The tool enhances the reliability of sequence alignments by addressing pyrosequencing-specific error types.
  • FAAST offers a fast and accurate solution for analyzing high throughput pyrosequencing data, available at http://www.ifm.liu.se/bioinfo/.