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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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Who is Who? Non-invasive Methods to Individually Sex and Mark Altricial Chicks
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Quail Genomics: a knowledgebase for Northern bobwhite.

Arun Rawat1, Kurt A Gust, Mohamed O Elasri

  • 1University of Southern Mississippi, Department of Biological Sciences, Hattiesburg, MS, USA.

BMC Bioinformatics
|October 16, 2010
PubMed
Summary

The Quail Genomics knowledgebase offers a central hub for Northern bobwhite (Colinus virginianus) genomic data, including a scaffold builder pipeline for enhanced analysis of this non-model species.

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Area of Science:

  • Avian genomics
  • Functional genomics
  • Bioinformatics

Background:

  • Established the Quail Genomics knowledgebase (http://www.quailgenomics.info) for Northern bobwhite (Colinus virginianus) functional genomic data.
  • Addresses the limited genomic information available for this non-model species in public databases.
  • Aims to facilitate genomic analysis and curation for researchers.

Purpose of the Study:

  • To create a comprehensive, web-based platform for Northern bobwhite genomic data.
  • To enable functional interrogation and analysis of avian genomic sequences.
  • To provide a searchable repository with extensive annotations and data retrieval options.

Main Methods:

  • Sequenced Northern bobwhite cDNA library using 454 Life Sciences next-generation sequencing.
  • Assembled 478,142 raw ESTs into nucleotide and protein sequences, annotating 21,980 unigenes.
  • Developed a MySQL database for meta-data retrieval and a pipeline for scaffold generation using chicken protein databases.

Main Results:

  • Generated and curated 478,142 raw ESTs and 21,980 annotated unigenes.
  • Established a searchable database with functional and structural annotations, including Gene Ontology (GO) browser.
  • Developed a scaffold building pipeline to improve sequence contiguity for 71,384 unigenes.

Conclusions:

  • The Quail Genomics knowledgebase serves as a central repository for Northern bobwhite genomic data.
  • Provides a platform for functional genomic analysis with comprehensive annotations and a scaffold building pipeline.
  • Future builds will integrate Japanese quail data, expanding the platform for avian species research.