MagicLamp: a web server and software toolkit for targeted gene annotation of microbial functions

Authors

Garber, A., Viney, I. A., Merino, N., Ramirez, G., Pavia, M. J., McAllister, S. M., Sadeghpour, S., Manna, A., Kreger, M. L., Wolk, B., Eunwoo, K., Qu, J., Armbruster, C. R., Perez-Rodriguez, I.

Abstract

Genome and metagenome annotation tools designed for large databases are ill-suited to the discovery of specialized, ecologically relevant microbial functions. MagicLamp (https://github.com/Arkadiy-Garber/MagicLamp) is a modular command-line software toolkit that performs targeted functional gene annotation searches using curated collections of hidden Markov models (HMMs), each representing discrete microbial metabolic processes. MagicLamp is also available as a web server: https://midauthorbio.com/#magiclamp. This targeted approach enables sensitive and specific annotation of genes involved in defined microbial processes, allowing MagicLamp to serve as a dedicated repository for the annotation of specialized microbial functions currently overlooked in other databases and software. The server accepts unannotated genome assemblies or GenBank-formatted annotations to perform HMM-based searches against curated model sets with reproducible, model-specific bit-score thresholds. Automated results are returned as tabular summaries and interactive HTML reports containing cross-genome/metagenome comparisons.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 24 Jul 2026.

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