AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome

F. Legeai, S. Shigenobu, J. P. Gauthier, J. Colbourne, C. Rispe, O. Collin, S. Richards, Alexandra Wilson, T. Murphy, D. Tagu

Research output: Contribution to journalArticle

68 Citations (Scopus)

Abstract

AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. AphidBase strongly supported community cooperation and coordination in the curation of gene models during community annotation of the pea aphid genome. AphidBase can be accessed at http://www.aphidbase.com.

Original languageEnglish
Pages (from-to)5-12
Number of pages8
JournalInsect Molecular Biology
Volume19
Issue numberSUPPL. 2
DOIs
StatePublished - Mar 1 2010

Fingerprint

Aphids
Acyrthosiphon pisum
Peas
Computational Biology
bioinformatics
Genome
genomics
genome
information systems
engines
Aphidoidea
Search Engine
Genomics
Information Systems
organisms
Software
Databases
genes
Genes

Keywords

  • Annotation
  • AphidBase
  • GMOD
  • Manual curation
  • Pea aphid genome

ASJC Scopus subject areas

  • Insect Science
  • Molecular Biology
  • Genetics

Cite this

Legeai, F., Shigenobu, S., Gauthier, J. P., Colbourne, J., Rispe, C., Collin, O., ... Tagu, D. (2010). AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome. Insect Molecular Biology, 19(SUPPL. 2), 5-12. https://doi.org/10.1111/j.1365-2583.2009.00930.x

AphidBase : A centralized bioinformatic resource for annotation of the pea aphid genome. / Legeai, F.; Shigenobu, S.; Gauthier, J. P.; Colbourne, J.; Rispe, C.; Collin, O.; Richards, S.; Wilson, Alexandra; Murphy, T.; Tagu, D.

In: Insect Molecular Biology, Vol. 19, No. SUPPL. 2, 01.03.2010, p. 5-12.

Research output: Contribution to journalArticle

Legeai, F, Shigenobu, S, Gauthier, JP, Colbourne, J, Rispe, C, Collin, O, Richards, S, Wilson, A, Murphy, T & Tagu, D 2010, 'AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome', Insect Molecular Biology, vol. 19, no. SUPPL. 2, pp. 5-12. https://doi.org/10.1111/j.1365-2583.2009.00930.x
Legeai F, Shigenobu S, Gauthier JP, Colbourne J, Rispe C, Collin O et al. AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome. Insect Molecular Biology. 2010 Mar 1;19(SUPPL. 2):5-12. https://doi.org/10.1111/j.1365-2583.2009.00930.x
Legeai, F. ; Shigenobu, S. ; Gauthier, J. P. ; Colbourne, J. ; Rispe, C. ; Collin, O. ; Richards, S. ; Wilson, Alexandra ; Murphy, T. ; Tagu, D. / AphidBase : A centralized bioinformatic resource for annotation of the pea aphid genome. In: Insect Molecular Biology. 2010 ; Vol. 19, No. SUPPL. 2. pp. 5-12.
@article{76971975b48340818d4cd076717e2123,
title = "AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome",
abstract = "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. AphidBase strongly supported community cooperation and coordination in the curation of gene models during community annotation of the pea aphid genome. AphidBase can be accessed at http://www.aphidbase.com.",
keywords = "Annotation, AphidBase, GMOD, Manual curation, Pea aphid genome",
author = "F. Legeai and S. Shigenobu and Gauthier, {J. P.} and J. Colbourne and C. Rispe and O. Collin and S. Richards and Alexandra Wilson and T. Murphy and D. Tagu",
year = "2010",
month = "3",
day = "1",
doi = "10.1111/j.1365-2583.2009.00930.x",
language = "English",
volume = "19",
pages = "5--12",
journal = "Insect Molecular Biology",
issn = "0962-1075",
publisher = "Wiley-Blackwell",
number = "SUPPL. 2",

}

TY - JOUR

T1 - AphidBase

T2 - A centralized bioinformatic resource for annotation of the pea aphid genome

AU - Legeai, F.

AU - Shigenobu, S.

AU - Gauthier, J. P.

AU - Colbourne, J.

AU - Rispe, C.

AU - Collin, O.

AU - Richards, S.

AU - Wilson, Alexandra

AU - Murphy, T.

AU - Tagu, D.

PY - 2010/3/1

Y1 - 2010/3/1

N2 - AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. AphidBase strongly supported community cooperation and coordination in the curation of gene models during community annotation of the pea aphid genome. AphidBase can be accessed at http://www.aphidbase.com.

AB - AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. AphidBase strongly supported community cooperation and coordination in the curation of gene models during community annotation of the pea aphid genome. AphidBase can be accessed at http://www.aphidbase.com.

KW - Annotation

KW - AphidBase

KW - GMOD

KW - Manual curation

KW - Pea aphid genome

UR - http://www.scopus.com/inward/record.url?scp=77954226464&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77954226464&partnerID=8YFLogxK

U2 - 10.1111/j.1365-2583.2009.00930.x

DO - 10.1111/j.1365-2583.2009.00930.x

M3 - Article

C2 - 20482635

AN - SCOPUS:77954226464

VL - 19

SP - 5

EP - 12

JO - Insect Molecular Biology

JF - Insect Molecular Biology

SN - 0962-1075

IS - SUPPL. 2

ER -