Specialized Annotation - Genomic Islands
Phage_Finder
Phage_Finder
- was created to identify prophage regions in completed bacterial
genomes. Using a test dataset of 42 bacterial genomes whose prophages
have been manually identified, Phage_Finder found 91% of the regions,
resulting in 7% false positive and 9% false negative prophages. A search
of 302 complete bacterial genomes predicted 403 putative prophage
regions, accounting for 2.7% of the total bacterial DNA. Analysis of the
285 putative attachment sites revealed tRNAs are targets for integration
slightly more frequently (33%) than intergenic (31%) or intragenic (28%)
regions, while tmRNAs were targeted in 8% of the regions.
(Reference: D.E. Fouts. 2006. Nucleic Acids Res. 34:
5839-5851).
ProphET
ProphET - ProphET identifies prophages in three steps: similarity search,
calculation of the density of prophage genes, and edge refinement.
ProphET performance was evaluated and compared with other phage predictors
based on a set of 54 bacterial genomes containing 267 manually annotated
prophages.This tool is part of
TAMU Galaxy
suite
(Reference: João L. Reis-Cunha J.L. et al. 2019.
PLOS ONE, 14 (10): e0223364).
PhageBoost
PhageBoost
- predicts prophages in a bacterial genomes and metagenomic contigs based
on biological features without sequence similarities
(Reference: Sirén K et al (2021) NAR Genom Bioinform
3(1): lqaa109).
PHASTEST
PHASTEST
PHAge Search Tool for Enhanced Sequence Translation - is designed to
support the rapid identification, annotation and visualization of prophage
sequences within bacterial genomes and plasmids. PHASTEST also supports
extensive annotation and interactive visualization of all other genes
(protein coding regions, tRNA sequences and rRNA sequences) in those same
genomes.
(Reference: Wishart D et al. Nucleic Acids Res.
(2023) 51(W1): W443-W450.).
Prophage Hunter
Prophage Hunter
- provides a one-stop web service to extract prophage genomes from
bacterial genomes, evaluate the activity of the prophages, identify
phylogenetically related phages, and annotate the function of phage
proteins.
(Reference: Song W et al. (2019) Nucleic Acids Res
47(W1): W74-W80).
IslandViewer
IslandViewer
- integrates four different genomic island prediction methods: IslandPick,
IslandPath-DIMOB, SIGI-HMM, and Islander
(Reference: Bertelli et al. 2017. Nucleic Acids Res.
45(W1): W30-W35).
PAIDB
PAIDB
(PAthogenicity Island DataBase) has made an effort to collect known PAIs
and to detect the potential PAI regions in the prokaryotic complete
genomes. Pathogenicity islands (PAIs) are distinct genetic elements of
pathogens encoding various virulence factors.
(Reference: Yoon SH et al. 2007. Nucleic Acids Res.
35 (Database Issue): D395-D400).
Mobile Genetic Elements - Not prophage
MOBHunter
MOBHunter
- mobile genetic elements (MGEs) range from small transposons to conspicuous integrative and conjugative elements. These
regions often confer advantageous traits, including antibiotic resistance or novel metabolic capabilities, and contain
foreign sequence signatures and hallmark genes such as transposases, integrases, etc. While bioinformatic tools target
specific MGE subsets using alignments, compositional signatures, or diagnostic gene mapping, no single platform offers a
unified framework for comprehensive, evidence-based, MGE identification and classification. MOBHunter is an advanced
bioinformatic pipeline that consolidates standalone tools and in-house algorithms.
(Reference: Rojas-Villalobos C et al. 2025. Nucleic Acids Research 53(W1): W398 - W407).
FinderIS
FinderIS -
is a dedicated database for bacterial insertion sequences (ISs). One of its functions is to assign IS names and to provide
a focal point for a coherent nomenclature. It is also the repository for ISs. Each new IS is indexed together with information
such as its DNA sequence and open reading frames or potential coding sequences, the sequence of the ends of the element and
target sites, its origin and distribution together with a bibliography where available. It provides BLASTn search capability.
(Reference: Siguier T et al. 2006. Nucleic Acids Res 34(Database issue): D32-36).
TnCentral
TnCentral -
ia a web resource for prokaryotic transposable elements (TE) including compound transposons; integrons; and associated
insertion sequences (IS). Its content can be browsed and queried through text- and sequence-based searches with a graphic
output.
(Reference: Ross K et al. 2021. mBio 12(5): e02060-21).
BacAnt
BacAnt -
which allows the annotation of antimicrobial resistance genes (ARGs), integrons and transposable elements at the same time.
The pipeline generates genbank files automatically, which are compatible with Easyfig for comparative genomic analysis.
(Reference: Hua X et al. 2021. Front Microbiol. 12: 649969).
RepetDB
RepetDB -
is designed to be a plant transposable elements (TE) knowledge base populated with full de novo TE annotations of complete (or near-complete) genome sequences. Indeed, the description and classification of TEs facilitates the exploration of specific TE families, superfamilies or orders across a large range of species. It also makes possible cross-species searches and comparisons of TE family content between genomes. Offers BLAST and text search capability. Free registration required.
(Reference: Amselem J et al. 2019. Mob DNA. 10: 6).
Updated: February, 2026