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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Related Experiment Video

Updated: Apr 12, 2026

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
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Bio301: A Web-Based EST Annotation Pipeline That Facilitates Functional Comparison Studies.

Yen-Chen Chen1, Yun-Ching Chen2, Wen-Dar Lin3

  • 1Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan.

ISRN Bioinformatics
|May 14, 2015
PubMed
Summary

Bio301 is a new website that helps researchers compare gene expression data. It offers tools for analyzing expressed sequence tags (ESTs) and selecting microarray probes, aiding biological discovery.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • The postgenomic era generates vast amounts of expressed sequence tag (EST) data for gene expression profiling.
  • Comparative gene expression studies are crucial for biological research.
  • Existing tools may lack user-friendliness or integrated comparison functionalities.

Purpose of the Study:

  • To develop a user-friendly EST annotation pipeline with integrated comparison tools.
  • To create a centralized platform (Bio301) for EST analysis and comparative studies.
  • To facilitate the mining of biological information from EST data.

Main Methods:

  • Construction of an integrated EST service website, Bio301.
  • Implementation of standard EST preprocessing and BLAST similarity searches.
  • Integration of Gene Ontology (GO) annotation, statistics reporting, and graphical GO browsing.
  • Development of microarray probe selection tools.
  • Inclusion of statistical library comparison functions based on GO annotations.

Main Results:

  • A comprehensive and user-friendly EST annotation pipeline is now available.
  • Bio301 provides integrated tools for EST preprocessing, annotation, and comparison.
  • The platform supports comparative analysis of multiple EST libraries using GO annotations.
  • Tools for microarray probe selection are incorporated.

Conclusions:

  • Bio301 enhances the ability of researchers to conduct comparative gene expression studies.
  • The integrated platform simplifies the analysis and interpretation of EST data.
  • Bio301 facilitates the discovery of meaningful biological insights through advanced data mining.