TerminatorNet uses a neural network to identify intrinsic (Rho-independent) transcription terminators in bacterial and archaeal genomic sequences. Understanding where transcripts end can be useful when investigating gene expression and regulation, and when determining whether a gene is co-expressed as part of a polycistronic operon.

Users may provide sequences for TerminatorNet to search. Alternatively, TerminatorNet includes a repository of tens of millions of terminators that it has identified in thousands of different genomes. A user can view and download from the repository all terminators identified in a genome.

As input, TerminatorNet requires one or more genomics sequences. If multiple sequences are submitted, the sequences should either be in FASTA format or else different sequences should be separated by blank lines. Sequences may contain either DNA or RNA nucleotides. For best results, sequences should be at least 50 nucleotides in length. TerminatorNet will search the submitted sequences for transcription terminators.

TerminatorNet also contains a repository of tens of millions of transcription terminators that it has identified in thousands of different genomes. All terminators identified by TerminatorNet in a given genome can be viewed and downloaded. When a user enters a few characters from the genome name, a drop-down box appears from which the user can select their genome of interest.

As output, TerminatorNet reports the terminators that it identifies in the provided genomic sequences. For each identified terminator, TerminatorNet reports the hairpin structure, the sequence upstream of the hairpin (Head), the sequence downstream of the hairpin (Tail), the energy of the hairpin (kcal/mol), TerminatorNet's confidence in the identification, the start coordinate of the hairpin within the provided sequence, and the stop coordinate of the hairpin within the provided sequence. For each terminator identified by TerminatorNet, a graphical image of the terminator's hairpin structure can be viewed by clicking on the terminator.

For terminators in TerminatorNet's repository, additional information is reported for each terminator, beyond that described above, including the genomic strand of the terminator, the name of the closest annotated gene for which the terminator may end transcription, an alternative (synonym) name for the gene, the distance from the terminator to the end of the gene (e.g., to the stop codon), and whether the terminator is upstream or downstream or overlaps the end of the gene (e.g., the stop codon).

The TerminatorNet repository contains millions of terminators from thousands of genomes. The repository does not contain terminators for all genomes. There are too many. If you are interested in using TerminatorNet to identify terminators throughout a genome other than those provided in the repository, you have two options.

Option #1. Download the source code and run TerminatorNet on your own machine.

Option #2. We do our best to support reasonable requests for individual genomes to be added to the TerminatorNet repository. We receive many such requests, so we kindly ask for your understanding and patience . Unfortunately, we cannot process batch requests, e.g., "please add these 20 genomes." If you would like to request that a genome be added to the repository, please follow these steps:

TerminatorNet source code is available on GitHub

A manuscript describing TerminatorNet is currently under review. Please check back at a later date for citation information.