Top 10 Best Gene and Genome Annotation Tools & Software

A process of identifying functional elements along a sequence of genome that assigns a meaning to it is called genome annotation. This process is necessary because DNA produces sequences of both known and unknown functions.

In the past three decades it has improved due to computational annotation of protein coding genes on single genomes.

It is a multi-step process that is accomplished by the help of multiple tools based on genome analysis. In this article we have highlighted the best gene and genome annotation tools for the purpose of gene functions identification.

What are The Best Gene & Genome Annotation Software and Tools?

Many complex steps are involved in this process for which very sophisticated tools are needed. Hence, the best tools are handpicked by us based on their performance, availability, and citation in reputed published researches.

We shall now describe the best gene and genome annotation tools and software used for every step in the next section.

For Identification of RNA Genes

1. RNAmmer

RNAmmer is a genome annotation computational predictor’s tool for major rRNA species from different kingdoms of organisms. The program is based on hidden Markov model that trains on 5S ribosomal RNA database and European ribosomal RNA database project.

A pre-screening step occurs in the tool that speeds up the process and losses very little sensitivity. It offers analysis of complete bacterial genome within a minute of execution. On running RNAmmer on large set of genomes, very high level of accuracy can be expected.

Many genomes give results for novel and unannotated rRNAs. The tool is available at the CBS server along with the genome analysis results of some executed functions. Available for academic download when larger input files.

  • Predicts 5s/8s, 16s/18s, 23s/28s ribosomal RNA in full genome sequences
  • The input files are in fasta format for single or multiple sequences
  • Output format is GFF, also in XML, HMM, FASTA
  • Parameters to choose kingdom- Archaea, bacteria, eukaryotes

2. tRNAScanSE

tRNAScanSE is a de facto software for prediction of tRNA genes in entire genomes. It has incorporated advanced methodologies with probabilistic search software. Available at online web server and also on UNIX-based commands line.

Widely accepted tool for last two decades. The parameters for search options are several such as sequence source, mode of search, type of query sequence (formatted/raw), output BED format and more.

Some additional executions options are to disable peusdo gene checking, show origin of first-pass hits, and to show the primary and secondary structure components to scores. The choice for genetic code for tRNA isotype prediction is offered. Users can give a cutoff score value.

  • Greatly adopted tool for finding tRNA genes in known/unknown sequences
  • Varied range of parameters are available to perform search
  • Standard output in the form of a list of genes in tabular format
  • Additional results can be generated using command line options

For Finding Genes/ORFs

3. Prodigal

Prodigal is a prokaryotic gene recognition and translation initiation site identification tool. It is based on prokaryotic dynamic programming gene finding algorithm. It provides better gene structure prediction, improvement in translation initiation site recognition and reduction in false positives.

Data is fed on initiation codon usage ATG vs GTG vs TTG, ribosomal binding site, motif usage, GC frame plot bias, hexamer coding statistics for complete training profile. It has a greater sensitivity in identifying existing genes accurately.

Used for annotation of microbial genomes submitted to GeneBank. Also incorporated in Swiss Institute of bioinformatics microbial genomics browser. Valuable source for annotation of either drafts or finished sequence of microbes.

  • A fast, lightweight and open source gene prediction program
  • The output consist of list of genes coordinates and protein translations
  • Detailed information about potential start in the genome
  • Can be run into two steps- training phase and prediction phase
  • Can be run in single step where training is hidden and final genes are obtained

4. GeneMark

GeneMark A combination of several gene prediction programmes developed at Georgia Institute of technology, USA. An effective tool for prediction of genes in varied organisms such as prokaryotes, eukaryotes, viruses, phages, plasmids and transcripts.

It is available for download and local installation. Based on hidden Markov model and heuristic algorithms. It is a part of genome annotation pipelines at NCBI, JGI, Broad Institute.

Several tools are integrated in this package such as- QUAST, MetAMOS, MAKER2, BRAKER1, and BRAKER2. Quite a popular and free bioinformatics tool used for different types of annotation functions.

  • Available software package- QUAST for quality assessment of genome assemblies
  • MetAMOS for metagenomic assembly analysis
  • MAKER2 for eukaryotic genome annotation
  • BRAKER1 for RNA-seq based eukaryotic genome annotations
  • BRAKER2 for protein based eukaryotic genome annotation pipeline

5. MetageneAnnotator

Metagene Annotator is comprehensive gene prediction tool that precisely predicts genes in prokaryotes from single set of anonymous genomic sequences of different lengths. MGA has statistical models of prophage genes integrated into it along with bacterial and archaeal genes.

Metagene Annotator can be downloaded on Linux and MacOS platforms. The input sequences should be less than 10 MBP in size for the web server. Only fastA format sequences are taken as input.

It also takes self-training model from input sequences for predictions. The output includes the name of sequence, GC content in percentage, RBS, Gene ID, and the positions of detection. Widely accepted for microbial genome studies and genome annotations.

  • Sensitive tool for detection of typical and atypical genes
  • Analyses Ribosomal Binding Sites RBS
  • Enables detection of a species specific patterns via RBS
  • Precisely predicts Translation starts of genes
  • Successful in improving prediction accuracy is for short sequences using RBS models

Also Check:

6. GrailEXP

GrailEXP is a Gene Recognition and Analysis Internet Link (GRAIL) that is popularly used systems for evaluation of the protein-coding potential of unknown DNA sequences.

Computational Biosciences dept at Oak Ridge National Laboratory employ it for the annotation of entire human genome. The tool also applies for microbial genome annotation and analysis.

The XGRAIL and genQuest are client-server applications used to locate exons on DNA sequences. Used to develop gene models and database search for homologs. Several parameters can be adjusted by the user before execution.

  • Flexibility in input parameters- selection of organism, output format, searching database
  • Input DNA sequence either raw or fasta format
  • Output formats- Raw GrailEXP format, genome channel, human-readable text
  • Varied gene modeling organism choices available
  • Extended choice for Cpg Islands, Gawain gene models and repetitive elements

For BLAST Searches


GenBank is a database for genetic sequences, all annotated collection and publicly available data. GenBank is maintained by INSDC that includes DNA data from DDBJ, ENA, and GenBank at NCBI. Data exchange is very frequent among these organizations.

There are multiple ways to retrieve data from GenBank- Entrez Nucleotide for sequence identifiers and annotations. BLAST for local alignment sequence searches, NCBI e-utilities for downloading sequences and more.

The most updated and scientifically accurate data is available here. After finding ORFs/ genes, GenBank can be used to find similar sequences to the genetic region of the unknown organism.

  • Comprehensively DNA data represented
  • Up-to-date and latest data available
  • Open source- free and public repository
  • Various operations- BLAST, deposition of data, retrieval done
  • Easy methods and multiple choices for searching data

8. UniProt

UniProt is an online facility for several tasks based on bioinformatics. It is maintained by EMBL-EBI the Swiss Institute of Bioinformatics and Protein Information Resource (PIR). A very comprehensive tool for protein sequence and annotation data.

External sources submit data to UniProt from where it is archived and revised. The UniProtKB is the protein knowledgebase that receives revised files from the archive.

In UniProtKB, automatically annotated data is generated by TrEMBL which is then exported to Swiss-Prot for review and manual annotation. The different repositories such as Proteomes constitutes the protein sets expressed by organisms and UniRef that has sequence clusters.

  • Rich collection of annotated and reviewed data of protein and DNA sequences
  • Multiple sources send data to UniProt, data accuracy enhances
  • Heavily cross-referenced and connected to several sources
  • Open-source bioinformatics platform for public use

For Metabolic Pathways

9. KEGG database

KEGG database is a source for information based on high-level functions and utilities of biological systems- cells, organisms, and ecosystem, from genomic, molecular and chemical data. A computational representation for systems, with genes and proteins as building blocks.

Data is integrated with wiring diagrams of interaction, biochemical reactions, and relation networks. Disease and drugs information is present too. There are several categories of database for clear demarcations.

A very special feature called KEGG Orthology system is the basis for genome annotation and mapping. Organism specific pathways (metabolic reconstruction) is feasible. Using EC number, automatic matching of terms with the organisms can be done.

  • Encyclopaedia for information on genes and genomes
  • Clear cut representation of biological relations using intriguing diagrams
  • Diseases and drugs study is very smooth
  • Annotated information for every organism
  • Integrated with several outside sources

For Protein Domain Search

10. InterProScan

InterProScan is an annotation source that provides information on functional analysis of protein sequences by classification into families. It predicts protein domains and important sites.

Open source with key values of heavy integration with diagnostic tool. Rich functional annotation and addition of relevant GO terms for automatic annotation of million GO terms across protein databases.

It uses predictive models called signatures (provided by member databases) that form the consortium. Incudes database- CATH, HAMAP, CDD, SMART, SFLD, SUPERFAMILY, TIGRfams, Prosite, PRINTS, Pfam, Panther, MobiDB Lite, and PIRSF.

  • Updated every two months, latest information available
  • Open source and free to use by science community
  • Intuitive website for easy navigation by beginners
  • Results can be obtained regarding protein families, domains and sites
  • Sequence search or InterPro annotations browsing is offered

Annotation is not a single step process, hence each executions must be carried out cautiously to avoid false positives at the end. In this article, we have categorically mentioned the best gene and genome annotation tools at different steps in the whole annotation process.

You may go for these free genome annotation tools to obtain best results in research. Each of them is expected to produce precise, accurate and sensitive data.

Leave a Reply

error: Content is protected !!