Welcome to DBsmORF!

DBsmORF is a database and web portal designed to help you identify small open reading frames (smORFs) in your microbial sequencing datasets. It accompanies the SmORFinder annotation tool and related manuscript. It is maintained by Matthew Durrant of the Bhatt Lab at Stanford University.

About

Download Tab

Use the form on this page to download pre-computed smORF predictions for thousands of RefSeq isolate genomes and HMP metagenomes. In its current form, you can filter the RefSeq genomes at various taxonomic levels, or by specificying an NCBI UID for a genome of interest. You can also specify how you want to filter the SmORFinder predictions based on two different significance filters. “Individual model significance filters” represent the significance cutoffs that must be met by at least one model to keep a given smORF prediction, and “Overlapping model significance filters” indicate the significance cutoffs that must be met by all three models to keep a given smORF prediction. You can preview your download by clicking the Preview button, and you can download by the data by clicking the Download button.

Annotate Tab

Use this form to annotate a genome or metagenome of interest on our server using the SmORFinder annotation tool. Just upload a FASTA nucleotide file of your genome/metagenome, indicate if it is an isolate genome or a metagenome, and specify the significance filters you want to use if they differ from the defaults. Click the Annotate button, and wait for your annotation to complete, and it will then been downloaded.

Ideally, you can do this on your own with the SmORFinder command line tool. This tool is easy to use and available for installation using pip.

Search Tab

This tab allows you to search for a given smORF in our database of RefSeq genomes and HMP metagenomes. Just enter the sequence of interest, the type of search to perform, and click Search. The results will indicate the species where related smORFs can be found, as well as the metagenomic body site.

smORF Families Tab

This tab provides summaries of smORF families for easy reference. It will automatically update the smORF based on what is selected from the dropdown menu, or the smorfam highlighted in a row of a the BLAST results table.

Issues and Questions

Please submit any issues or questions that you may have with DBsmORF or the SmORFinder software on the issues page of the SmORFinder github repository.

Cite our work

Please cite these two papers if you use DBsmORF or SmORFinder:

Durrant, Matthew G., and Ami S. Bhatt. 2020. “Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes.” Cell Host & Microbe, December. https://doi.org/10.1016/j.chom.2020.11.002.

Sberro, Hila, Brayon J. Fremin, Soumaya Zlitni, Fredrik Edfors, Nicholas Greenfield, Michael P. Snyder, Georgios A. Pavlopoulos, Nikos C. Kyrpides, and Ami S. Bhatt. 2019. “Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes.” Cell 178 (5): 1245–59.e14.

Download Pre-computed Annotations

Individual model significance filters

Overlapping model significance filters

Download

Individual model significance filters

Overlapping model significance filters

Annotate

Annotate your data yourself!

We have developed an easy-to-use command line tool for you to annotate smORFs in your own sequenced genomes and metagenomes. We recommend you use this tool, especially for larger analyses. You can install the SmORFinder command line tool from a unix terminal using the command:

pip install smorfinder

You can annotate a single isolate genome using a command such as:

smorf single mygenome.fna

And you can annotate a metagenome with a command such as:

smorf meta --threads 8 mymetagenome.fna

For more information, please reference the github repository and wiki.

Otherwise, feel free to try out the Web Server implementation of the SmORFinder annotation tool on the next tab.

Analyze smORF Families