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

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.

2026-07-22 bioinformatics
10.64898/2026.07.19.739457 bioRxiv
Show 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.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.