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 Videos

EGene: a configurable pipeline generation system for automated sequence analysis.

Alan M Durham1, André Y Kashiwabara, Fernando T G Matsunaga

  • 1Depto. de Ciências da Computação, Instituto de Matemática e Estatística São Paulo, SP, 05508-900, Brazil. alan@ime.usp.br

Bioinformatics (Oxford, England)
|April 9, 2005
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

RdDM-Associated Chromatin Remodelers in Soybean: Evolution and Stress-Induced Expression of CLASSY Genes.

Plants (Basel, Switzerland)·2025
Same author

Integrating Sequence- and Structure-Based Similarity Metrics for the Demarcation of Multiple Viral Taxonomic Levels.

Viruses·2025
Same author

ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages.

GigaScience·2024
Same author

Rational Design of Profile HMMs for Sensitive and Specific Sequence Detection with Case Studies Applied to Viruses, Bacteriophages, and Casposons.

Viruses·2023
Same author

Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and pre-processing bias in classification of mock bacterial community samples.

PloS one·2023
Same author

Characterization of a Novel Mitovirus of the Sand Fly <i>Lutzomyia longipalpis</i> Using Genomic and Virus-Host Interaction Signatures.

Viruses·2020

EGene simplifies bioinformatics pipeline construction using a modular system and visual tools. It integrates third-party programs without requiring programming experience, aiding sequence processing tasks.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Traditional pipeline construction can be complex and require programming expertise.
  • Integrating diverse third-party tools into a cohesive workflow presents challenges.

Purpose of the Study:

  • To introduce EGene, a flexible and modular pipeline generation system.
  • To enable seamless integration of third-party programs for distinct bioinformatics projects.
  • To provide a user-friendly tool for pipeline construction and documentation.

Main Methods:

  • EGene employs a modular design for pipeline generation.
  • It integrates with third-party programs without necessitating prior programming knowledge.
  • CoEd, a visual tool, facilitates pipeline construction and documentation.

Related Experiment Videos

Main Results:

  • EGene offers a generic and flexible system for creating bioinformatics pipelines.
  • It supports the integration of various components for sequence processing.
  • CoEd enhances usability and simplifies documentation.

Conclusions:

  • EGene democratizes pipeline construction in bioinformatics, making it accessible to users without programming backgrounds.
  • The system's modularity and visual interface streamline the development of custom sequence processing workflows.