Table · dataset · 2026
MetaproDB: A Flexible and Reproducible Framework for Biome-Informed Protein Sequence Database Construction for Metaproteomics
Listed in figshare
Metaproteomic analyses commonly rely on protein sequence databases, yet database construction remains one of the most variable steps in metaproteomic workflows.
Description
Here, I present MetaproDB, a flexible and reproducible framework for biome-informed protein-sequence-database construction in metaproteomics. MetaproDB integrates ecological taxon selection, build-plan generation, genome resource linkage, protein sequence assembly, exact-sequence deduplication, completeness assessment, and provenance tracking within a unified workflow.
It supports both database generation from a curated reference panel of representative biomes and cohort-specific construction from user-provided microbiome profiles. I demonstrate the functionality of MetaproDB through three case studies that compare different database construction strategies. MetaproDB provides a practical framework for explicit and reproducible biome-informed database design in metaproteomics and is available at [github.com/arikanlab/MetaproDB].
Links
Where it is published
- DOI doi.org/10.1021/acs.jproteome.6c00326.s002 ↗
DOI / persistent id · from figshare com
Catalogue records · 1
- OAI-PMH record api.figshare.com/v2/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3Af… ↗
metadata API · from figshare com
Topics
Provenance · 1 source records, 20 field assertions
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| description | source · figshare com | connector:figshare_com@1.0.0 | /metadata/dc/description |
| license | source · figshare com | connector:figshare_com@1.0.0 | /metadata/dc/rights |
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| title | source · figshare com | connector:figshare_com@1.0.0 | /metadata/dc/title |