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Quail Genomics: a knowledgebase for Northern bobwhite

BACKGROUND: The Quail Genomics knowledgebase (http://www.quailgenomics.info) has been initiated to share and develop functional genomic data for Northern bobwhite (Colinus virginianus). This web-based platform has been designed to allow researchers to perform analysis and curate genomic information...

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Detalles Bibliográficos
Autores principales: Rawat, Arun, Gust, Kurt A, Elasri, Mohamed O, Perkins, Edward J
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3026360/
https://www.ncbi.nlm.nih.gov/pubmed/20946596
http://dx.doi.org/10.1186/1471-2105-11-S6-S13
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author Rawat, Arun
Gust, Kurt A
Elasri, Mohamed O
Perkins, Edward J
author_facet Rawat, Arun
Gust, Kurt A
Elasri, Mohamed O
Perkins, Edward J
author_sort Rawat, Arun
collection PubMed
description BACKGROUND: The Quail Genomics knowledgebase (http://www.quailgenomics.info) has been initiated to share and develop functional genomic data for Northern bobwhite (Colinus virginianus). This web-based platform has been designed to allow researchers to perform analysis and curate genomic information for this non-model species that has little supporting information in GenBank. DESCRIPTION: A multi-tissue, normalized cDNA library generated for Northern bobwhite was sequenced using 454 Life Sciences next generation sequencing. The Quail Genomics knowledgebase represents the 478,142 raw ESTs generated from the sequencing effort in addition to assembled nucleotide and protein sequences including 21,980 unigenes annotated with meta-data. A normalized MySQL relational database was established to provide comprehensive search parameters where meta-data can be retrieved using functional and structural information annotation such as gene name, pathways and protein domain. Additionally, blast hit cutoff levels and microarray expression data are available for batch searches. A Gene Ontology (GO) browser from Amigo is locally hosted providing 8,825 unigenes that are putative orthologs to chicken genes. In an effort to address over abundance of Northern bobwhite unigenes (71,384) caused by non-overlapping contigs and singletons, we have built a pipeline that generates scaffolds/supercontigs by aligning partial sequence fragments against the indexed protein database of chicken to build longer sequences that can be visualized in a web browser. CONCLUSION: Our effort provides a central repository for storage and a platform for functional interrogation of the Northern bobwhite sequences providing comprehensive GO annotations, meta-data and a scaffold building pipeline. The Quail Genomics knowledgebase will be integrated with Japanese quail (Coturnix coturnix) data in future builds and incorporate a broader platform for these avian species.
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spelling pubmed-30263602011-01-26 Quail Genomics: a knowledgebase for Northern bobwhite Rawat, Arun Gust, Kurt A Elasri, Mohamed O Perkins, Edward J BMC Bioinformatics Proceedings BACKGROUND: The Quail Genomics knowledgebase (http://www.quailgenomics.info) has been initiated to share and develop functional genomic data for Northern bobwhite (Colinus virginianus). This web-based platform has been designed to allow researchers to perform analysis and curate genomic information for this non-model species that has little supporting information in GenBank. DESCRIPTION: A multi-tissue, normalized cDNA library generated for Northern bobwhite was sequenced using 454 Life Sciences next generation sequencing. The Quail Genomics knowledgebase represents the 478,142 raw ESTs generated from the sequencing effort in addition to assembled nucleotide and protein sequences including 21,980 unigenes annotated with meta-data. A normalized MySQL relational database was established to provide comprehensive search parameters where meta-data can be retrieved using functional and structural information annotation such as gene name, pathways and protein domain. Additionally, blast hit cutoff levels and microarray expression data are available for batch searches. A Gene Ontology (GO) browser from Amigo is locally hosted providing 8,825 unigenes that are putative orthologs to chicken genes. In an effort to address over abundance of Northern bobwhite unigenes (71,384) caused by non-overlapping contigs and singletons, we have built a pipeline that generates scaffolds/supercontigs by aligning partial sequence fragments against the indexed protein database of chicken to build longer sequences that can be visualized in a web browser. CONCLUSION: Our effort provides a central repository for storage and a platform for functional interrogation of the Northern bobwhite sequences providing comprehensive GO annotations, meta-data and a scaffold building pipeline. The Quail Genomics knowledgebase will be integrated with Japanese quail (Coturnix coturnix) data in future builds and incorporate a broader platform for these avian species. BioMed Central 2010-10-07 /pmc/articles/PMC3026360/ /pubmed/20946596 http://dx.doi.org/10.1186/1471-2105-11-S6-S13 Text en Copyright ©2010 Perkins et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Proceedings
Rawat, Arun
Gust, Kurt A
Elasri, Mohamed O
Perkins, Edward J
Quail Genomics: a knowledgebase for Northern bobwhite
title Quail Genomics: a knowledgebase for Northern bobwhite
title_full Quail Genomics: a knowledgebase for Northern bobwhite
title_fullStr Quail Genomics: a knowledgebase for Northern bobwhite
title_full_unstemmed Quail Genomics: a knowledgebase for Northern bobwhite
title_short Quail Genomics: a knowledgebase for Northern bobwhite
title_sort quail genomics: a knowledgebase for northern bobwhite
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3026360/
https://www.ncbi.nlm.nih.gov/pubmed/20946596
http://dx.doi.org/10.1186/1471-2105-11-S6-S13
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