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Annotation evaluation software tools | Genome annotation

Genome-wide functional annotation either by manual or automatic means has raised considerable concerns regarding the accuracy of assignments and the reproducibility of methodologies. In addition, a performance evaluation of automated systems that…
AEGeAn
Desktop

AEGeAn Analysis and Evaluation of Genome Annotations

Permits to manage and analyze whole-genome gene structure annotations. AEGeAn…

Permits to manage and analyze whole-genome gene structure annotations. AEGeAn leverages a variety of parsers, data structures, and graphics capabilities. It is composed of different tools like…

ParsEval
Desktop

ParsEval

Allows pairwise comparison of sets of gene structure annotations. ParsEval is…

Allows pairwise comparison of sets of gene structure annotations. ParsEval is able to analyze annotations for large eukaryotic genomes. It calculates several statistics that highlight the…

CGL
Desktop

CGL Comparitive Genomics Library

A suite of measures for annotation management to characterize change to a…

A suite of measures for annotation management to characterize change to a genome's annotations between releases. CGL provides an easy means to explore, compare, and characterize genome…

Annotation…
Desktop

Annotation issues

An inference system to check for violations of constraints in gene ontology…

An inference system to check for violations of constraints in gene ontology (GO) annotations. Annotation issues automatically finds inconsistencies between the implicit taxon specificity of GO…

Eval
Desktop

Eval

Analyzes the performance of gene annotation systems. Eval provides summaries…

Analyzes the performance of gene annotation systems. Eval provides summaries and graphical distributions for many descriptive statistics about any set of annotations, regardless of their source. It…

GFPE
Desktop

GFPE Gene-Finding Program Evaluation

A set of Java classes for evaluating gene-finding programs. GFPE calculates a…

A set of Java classes for evaluating gene-finding programs. GFPE calculates a number of metrics of accuracy of predictions at three levels:the coding level, the exon level, and the protein level.

Meta…
Desktop

Meta A(nnotator)

Generates new functional descriptors from the annotation of a given entry using…

Generates new functional descriptors from the annotation of a given entry using the semantic units of the annotation as prepositions for implications executed in accordance with the rule library.…

AraSet
Dataset

AraSet

Enables the evaluation of multi-gene models for the Arabidopsis genome. AraSet…

Enables the evaluation of multi-gene models for the Arabidopsis genome. AraSet is a data set of contigs of validated genes and contains 566 014 nucleotides divided in 74 loci. It is composed of 57,…

ACS
Desktop

ACS Annotation Confidence Score

An annotation quality scoring scheme to reduce the cost for microbial genomes…

An annotation quality scoring scheme to reduce the cost for microbial genomes annotation. ACS is computed by combining sequence and textual annotation similarity using a modified version of a…

AnnoComp
Desktop

AnnoComp Annotation Comparison

A semi-automated scheme capable of comparing functional annotations from…

A semi-automated scheme capable of comparing functional annotations from different sources and consequently obtaining a consensus genome functional annotation result. AnnoComp reduces the manual work…

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