CEGMA

CEGMA identifies and maps a conserved set of core eukaryotic genes (CEGs) to annotate exon–intron structures in draft eukaryotic genome assemblies and to assess completeness of gene catalogs.

Key Features:

• Core gene set: defines a set of highly conserved protein families (core eukaryotic genes, CEGs) prevalent across diverse eukaryotic organisms.
• Low-copy markers: targets CEGs characterized by extreme conservation and low copy numbers in higher eukaryotes to serve as reliable single-copy markers.
• Profile HMMs: employs profile-hidden Markov models (HMMs) to detect conserved protein families in genomic sequences.
• Exon–intron mapping: uses a mapping procedure to identify exon–intron structures of conserved protein families within novel genomic sequences.
• Initial gene annotations: constructs an initial set of reliable gene annotations in draft-stage genomes.
• Assembly completeness metric: reports the proportion of CEGs mapped within a draft genome to evaluate completeness of gene catalogs.
• Gene-finder training and validation: provides annotations useful for training gene-finding algorithms and validating automatic predictions.
• Complementary metrics: complements N50 length and x-fold coverage by directly assessing gene space in assemblies.

Scientific Applications:

• Assembly quality assessment: assessing the completeness of gene catalogs in draft eukaryotic genome assemblies.
• Gene-prediction development: training and validating gene-finding algorithms using conserved gene annotations.
• Comparative assembly metrics: providing a gene-space-based complement to N50 length and x-fold coverage for sequencing and assembly evaluation.
• Initial annotation in low-data projects: generating initial reliable gene annotations when experimental evidence is limited or absent.

Methodology:

Defines a set of highly conserved protein families (CEGs), builds and applies profile-hidden Markov models (HMMs) to map those families to genomic sequences, uses a mapping procedure to identify exon–intron structures, and reports the proportion of CEGs mapped as an assembly completeness metric.