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PipeOnline 2.0: automated EST processing and functional data sorting.

Patricia Ayoubi1, Xiaojing Jin, Saul Leite

  • 1Department of Microbiology and Molecular Genetics and. School of Mechanical and Aerospace Engineering, Oklahoma State University, Stillwater, OK 74078, USA.

Nucleic Acids Research
|November 1, 2002
PubMed
Summary

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PipeOnline is a new bioinformatics tool that analyzes raw DNA sequence data, transforming it into a valuable, annotated database of unigene expressed sequence tags (ESTs) for biological research.

Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Expressed sequence tags (ESTs) are often deposited as redundant, unannotated data with limited biological content.
  • Efficient analysis of large-scale EST datasets is crucial for extracting meaningful biological information.

Purpose of the Study:

  • To introduce PipeOnline, an automated bioinformatics pipeline for processing and annotating raw DNA sequence data.
  • To convert raw ESTs into a curated, unigene dataset with functional annotations.

Main Methods:

  • Automated base calling, vector sequence screening, and removal.
  • Assembly of redundant ESTs into consensus unigene sequences.
  • Functional annotation using amino acid sequence homology and public databases.

Related Experiment Videos

Main Results:

  • PipeOnline generates an annotated database containing processed unigene sequences, clone history, sequence alignments, and functional classifications.
  • The system provides automated functional annotation based on a novel homology method.
  • Customizable features and an alert service are available through MyPipeOnline.

Conclusions:

  • PipeOnline offers a comprehensive solution for transforming raw ESTs into biologically relevant, annotated data.
  • The tool facilitates efficient data mining and functional exploration of genomic datasets.
  • PipeOnline enhances the utility of public sequence data for biological research.