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Prophinder is a tool dedicated to the detection of prophages in sequenced bacterial genomes.
The algorithm uses the coding sequences (CDS) that are similar (using BLASTP) to phage proteins stored in the ACLAME database. Genome regions with a significantly high density of these phage-like proteins are identified using the binomial formula and comparing to the number of such CDS expected by chance only. Based on the ACLAME annotations and biological knowledge integrated in the program, Prophinder selects the phage-like genes dense regions (PGDRs) best matching protential prophages. A number of parameters can be tweaked to optimise the prediction for a given genome.


The method is run regularly on newly sequenced bacterial genomes which are available for browsing on the web site. A web interface has been developed to submit your own GenBank formatted genome to the Prophinder program with numerous tools to visualise/analyse the results. Finally, a web service has been created to use Prophinder remotely.
Distributing Prophinder as a standalone application is not possible due to many dependencies. The web service should provide identical functionality with the advantage of always using the most up-to-date version of the program and annotations in the ACLAME database.

Available services

Pre-processed bacterial genomes
predictions in bacterial genomes.

Direct access by NC number

Access a prophage by its ID:
(e.g.: NC_003997:prophinder:34501 or prophinder:34501 or just 34501)

Direct access a prophage or a genome based on a with value

The value must be exact. If it matches a feature in a prophage, the detailed view of the prophage will be shown, the matching genome view otherwise.
Interactive tools

View prediction ID

Tools and description of the web service
Documentation Genome view description
Prophage view description
Genomic region view description
File formats description
Prophage ACLAME hits view

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