Genome annotation databases and software tools

Genome annotation applications

Functional TFBS identification

10 tools

Cis-regulatory DNA element data

14 tools

Mutational signature identification

2 tools

Protein-coding gene prediction

40 tools

Translational research platforms

8 tools

DNase I hypersensitive-site prediction

1 tools

Transposable element prediction

32 tools

The falling cost of genome sequencing is having a marked impact on the research community with respect to which genomes are sequenced and how and where they are annotated. Genome annotation projects have generally become small-scale affairs that are often carried out by an individual laboratory. Although annotating a eukaryotic genome assembly is now within the reach of non-experts, it remains a challenging task. Source text: Yandell and Ence, 2012.

Genome annotation applications

Genome data

Gene data

Annotation pipeline

Gene prioritization

Genome visualization

Promoter prediction

Enhancer prediction

Motif discovery

Motif enrichment

Motif scanning

Motif comparison

Functional TFBS identification

Genomic region enrichment

Cis-regulatory DNA element data

Super-enhancer data

SnoRNA gene prediction

Impact of variants on miRNAs

Genomic interval association

Genome assembly data

Taxonomy identification

Indel extraction

Mutational signature identification

tRNA gene prediction

Protein-coding gene prediction

Frameshift prediction

Absent word detection

CpG island prediction

Genomic island prediction

Chloroplast DNA data

Mitochondrial DNA data

Integron data

CRISPR prediction

miRNA precursor prediction

Intronless gene data

DNA triplex prediction

DNA triplex data

Gene visualization

Operon data

Data warehousing systems

Translational research platforms

DNase I hypersensitive-site prediction

Transposable element prediction

Transposable element data

Tandem repeat prediction

Tandem repeat data

Insertion sequence prediction

Prophage prediction