CEGMA

A pipeline to accurately annotate core genes in eukaryotic genomes

Genis Parra, Keith Bradnam, Ian F Korf

Research output: Contribution to journalArticle

1048 Citations (Scopus)

Abstract

Motivation: The numbers of finished and ongoing genome projects are increasing at a rapid rate, and providing the catalog of genes for these new genomes is a key challenge. Obtaining a set of wellcharacterized genes is a basic requirement in the initial steps of any genome annotation process. An accurate set of genes is needed in order to learn about species-specific properties, to train gene-finding programs, and to validate automatic predictions. Unfortunately, many new genome projects lack comprehensive experimental data to derive a reliable initial set of genes. Results: In this study, we report a computational method, CEGMA (Core Eukaryotic Genes Mapping Approach), for building a highly reliable set of gene annotations in the absence of experimental data. We define a set of conserved protein families that occur in a wide range of eukaryotes, and present a mapping procedure that accurately identifies their exon-intron structures in a novel genomic sequence. CEGMA includes the use of profile-hidden Markov models to ensure the reliability of the gene tructures. Our procedure allows one to build an initial set of reliable gene annotations in potentially any eukaryotic genome, even those in draft stages.

Original languageEnglish (US)
Pages (from-to)1061-1067
Number of pages7
JournalBioinformatics
Volume23
Issue number9
DOIs
StatePublished - May 2007

Fingerprint

Chromosome Mapping
Genome
Pipelines
Genes
Gene
Molecular Sequence Annotation
Annotation
Eukaryota
Introns
Experimental Data
Exons
Computational Methods
Markov Model
Genomics
Hidden Markov models
Computational methods
Proteins
Protein
Prediction

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Medicine(all)

Cite this

CEGMA : A pipeline to accurately annotate core genes in eukaryotic genomes. / Parra, Genis; Bradnam, Keith; Korf, Ian F.

In: Bioinformatics, Vol. 23, No. 9, 05.2007, p. 1061-1067.

Research output: Contribution to journalArticle

Parra, Genis ; Bradnam, Keith ; Korf, Ian F. / CEGMA : A pipeline to accurately annotate core genes in eukaryotic genomes. In: Bioinformatics. 2007 ; Vol. 23, No. 9. pp. 1061-1067.
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