Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Video

Updated: Apr 11, 2026

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

4.8K

FAST: FAST Analysis of Sequences Toolbox.

Travis J Lawrence1, Kyle T Kauffman2, Katherine C H Amrine3

  • 1Quantitative and Systems Biology Program, University of California, Merced Merced, CA, USA.

Frontiers in Genetics
|June 5, 2015
PubMed
Summary

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Reaction Optimization for Enzymatic Deconstruction of Industrially Relevant Nylon Composites.

Chembiochem : a European journal of chemical biology·2026
Same author

Circularity in Sequence-Controlled Copolyamides Enabled by Regioselective Enzymatic Hydrolysis.

Journal of the American Chemical Society·2026
Same author

Bacteria covalently incorporate polyfluoroalkyl carboxylates into membrane lipids.

Nature microbiology·2026
Same author

Structural and oligomeric characterization of substrate- and product-selective nylon hydrolases.

bioRxiv : the preprint server for biology·2026
Same author

Genomic signatures in <i>Variovorax</i> enabling colonization of the <i>Populus</i> endosphere.

mSystems·2026
Same author

A distinct subpopulation of membrane vesicles in <i>Pseudomonas putida</i> is enriched in enzymes for lignin catabolism.

Applied and environmental microbiology·2025
This summary is machine-generated.

FAST (FAST Analysis of Sequences Toolbox) offers open-source command-line tools for biological sequence analysis. These tools simplify bioinformatic workflows, enhancing data transparency and reproducibility for researchers.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Bioinformatic workflows often require complex scripting, hindering accessibility for non-programmers.
  • Existing tools may lack a unified, intuitive command-line interface for diverse sequence manipulation tasks.

Purpose of the Study:

  • To introduce the FAST (FAST Analysis of Sequences Toolbox), a suite of open-source command-line tools.
  • To provide biologists with accessible and powerful methods for filtering, transforming, annotating, and analyzing biological sequence data.
  • To enhance the reproducibility and transparency of bioinformatic protocols.

Main Methods:

  • FAST employs a command-line interface modeled after GNU Textutils (e.g., grep, cut, tr) with tools like fasgrep, fascut, and fastr.
  • It supports compact, combinatorial encoding of data workflows for rapid prototyping.
Keywords:
BioPerlMultiFASTANCBI taxonomyUnix philosophybioinformatic workflowopen sourcepipelineregular expression

More Related Videos

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

9.3K
3' End Sequencing Library Preparation with A-seq2
12:01

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

11.2K

Related Experiment Videos

Last Updated: Apr 11, 2026

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

4.8K
Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

9.3K
3' End Sequencing Library Preparation with A-seq2
12:01

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

11.2K
  • FAST automates analysis based on sequence content, features, and annotations, supporting various data formats including Multi-FastA and FastQ.

    • Main Results:

    • FAST enables efficient filtering, transformation, and annotation of biological sequence data.
    • The toolbox automates sorting, selection, and analysis of sequence records and alignment sites.
    • It supports molecular population genetics statistics and facilitates interactive data investigation.

    Conclusions:

    • FAST simplifies the creation and documentation of bioinformatic workflows, promoting transparency and reproducibility.
    • Its intuitive interface and broad functionality make complex sequence analysis more accessible to biologists.
    • The toolbox is portable, secure, and easy to install, built on mature Perl and BioPerl foundations.