EcoGene 3.0

Jindan Zhou, Kenneth E. Rudd

Research output: Contribution to journalArticle

124 Citations (Scopus)

Abstract

EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade include (i) graphic presentations of genome map features; (ii) ability to design Boolean queries and Venn diagrams from EcoArray, EcoTopics or user-provided GeneSets; (iii) the genome-wide clone and deletion primer design tool, PrimerPairs; (iv) sequence searches using a customized EcoBLAST; (v) a Cross Reference table of synonymous gene and protein identifiers; (vi) proteome-wide indexing with GO terms; (vii) EcoTools access to >2000 complete bacterial genomes in EcoGene-RefSeq; (viii) establishment of a MySql relational database; and (ix) use of web content management systems. The biomedical literature is surveyed daily to provide citation and gene function updates. As of September 2012, the review of 37 397 abstracts and articles led to creation of 98 425 PubMed-Gene links and 5415 PubMed-Topic links. Annotation updates to Genbank U00096 are transmitted from EcoGene to NCBI. Experimental verifications include confirmation of a CTG start codon, pseudogene restoration and quality assurance of the Keio strain collection.

Original languageEnglish
JournalNucleic Acids Research
Volume41
Issue numberD1
DOIs
StatePublished - Jan 1 2013
Externally publishedYes

Fingerprint

Genome
PubMed
Databases
Bacterial Genomes
Pseudogenes
Initiator Codon
Nucleic Acid Databases
Proteome
Genes
Clone Cells
Escherichia coli
Proteins

ASJC Scopus subject areas

  • Genetics

Cite this

EcoGene 3.0. / Zhou, Jindan; Rudd, Kenneth E.

In: Nucleic Acids Research, Vol. 41, No. D1, 01.01.2013.

Research output: Contribution to journalArticle

Zhou, J & Rudd, KE 2013, 'EcoGene 3.0', Nucleic Acids Research, vol. 41, no. D1. https://doi.org/10.1093/nar/gks1235
Zhou, Jindan ; Rudd, Kenneth E. / EcoGene 3.0. In: Nucleic Acids Research. 2013 ; Vol. 41, No. D1.
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