cff-version: 1.2.0
abstract: "<p>SAFPredDB is a bacterial synteny database built for the gene function prediction tool SAFPred, Synteny Aware Function Predictor. The database is a collection of conserved synteny and operons found across the bacterial kingdom. First, we formulated a synteny model based on experimentally known operons and the genomic features common in bacteria. We designed a bottoms-up, purely computational approach to build our database based on the proposed synteny model using complete bacterial genome assemblies from the Genome Taxonomy Database (GTDB).</p><p><br></p><p>Although we initially built SAFPred for our prediction tool only, it can be used for other purposes where such a catalog is needed. As a standalone database, it can be queried to mine information about conserved genomic patterns in bacteria. In addition, it can be updated as newer assemblies are added to GTDB.</p>"
authors:
  - family-names: Urhan
    given-names: Aysun
    orcid: "https://orcid.org/0000-0001-8584-4736"
  - family-names: Cosma
    given-names: Bianca-Maria
  - family-names: Earl
    given-names: Ashlee M.
    orcid: "https://orcid.org/0000-0001-7857-9145"
  - family-names: Manson
    given-names: Abigail L.
    orcid: "https://orcid.org/0000-0002-3800-0714"
  - family-names: Abeel
    given-names: Thomas
title: "SAFPredDB: Bacterial synteny database"
keywords:
version: 1
identifiers:
  - type: doi
    value: 10.4121/ac84802e-853f-46f1-9786-b9d29c0f7557.v1
license: CC BY-NC 4.0
date-released: 2024-04-05