HomAAR

HomAAR, short for Homology-Aware Annotation and Alignment Repository, is a software platform designed to assist researchers in comparative genomics and protein evolution studies. It provides an integrated environment to identify homologous sequences, construct alignments, infer phylogenies, and transfer or curate functional annotations across species. The project aims to streamline workflows from sequence discovery to annotation propagation, while preserving provenance and reproducibility.

Overview: Users can query sequence databases, run homology searches (for example BLAST and HMMER) against curated gene families, and assemble homolog clusters. The platform offers multiple sequence alignment tools (such as MAFFT and MUSCLE) and phylogenetic tree inference modules (including RAxML and FastTree), along with utilities to evaluate alignment quality and evolutionary relationships.

Data model and provenance: HomAAR stores gene models, alignments, trees, and annotations with versioning and audit trails. Annotations can be derived from external resources (GO, InterPro, Pfam) and can be manually curated within the interface. The system emphasizes traceability of annotation transfers between homologs, facilitating reproducible analyses.

Architecture and interoperability: Built as a modular, controller-driven web application with a REST API, it supports plugins and can be deployed locally or in cloud environments. Data can be imported from and exported to common formats (FASTA, GFF3, Newick) and integrated with external databases.

Applications: It is used for rapid functional annotation of draft genomes, comparative analyses of gene families, and evolutionary studies across model and non-model organisms.

Reception: The project is recognized for improving reproducibility in comparative genomics workflows and for enabling collaborative curation, though users should be mindful of potential biases in automated annotation transfer.

See also: OrthoDB, Ensembl Compara, OrthoFinder.