Evidence map›Paper›PMID 37333121›Full record

ArticlebioRxiv : the preprint server for biology2024

zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters.

Rauf Salamzade, Patricia Q Tran, Cody Martin, Abigail L Manson, Michael S Gilmore, Ashlee M Earl, Karthik Anantharaman, Lindsay R Kalan

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors.

Rauf SalamzadeDepartment of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.ORCID 0000-0002-1923-5948
Patricia Q TranDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.ORCID 0000-0003-3948-3938
Cody MartinMicrobiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.ORCID 0000-0001-7610-9537
Abigail L MansonInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.ORCID 0000-0002-3800-0714
Michael S GilmoreInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Ashlee M EarlInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Karthik AnantharamanDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.ORCID 0000-0002-9584-2491
Lindsay R KalanDepartment of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.ORCID 0000-0003-4980-5128

Funding

Viral Genomics: evolution, spread, and host interactionsU19AI110818 · NIAID · BROAD INSTITUTE, INC. · PI EARL, ASHLEE MIRIAM · 2014 to 2024
$66.5M
Novel antimicrobials targeting MDR pathogens from animal microbial symbiontsU19AI142720 · NIAID · UNIVERSITY OF WISCONSIN-MADISON · PI ANDES, DAVID R · 2019 to 2023
$30.1M
COMPUTATIONAL FRAMEWORKS FOR PHAGE DISCOVERY, ECOLOGY, AND DYNAMICS FROM METAGENOMESR35GM143024 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI ANANTHARAMAN, KARTHIK · 2021 to 2025
$1.9M
Elucidating the Role of Microbial Community Dynamics in Wound Repair and RegenerationR35GM137828 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI KALAN, LINDSAY ROBYN · 2020 to 2021
$750k
NIAID NIH HHS U19 AI110818NIAID NIH HHS U19 AI142720NIGMS NIH HHS R35 GM137828NIGMS NIH HHS R35 GM143024
6 · The paper itself

Abstract

Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic elements (MGEs), such as biosynthetic gene clusters (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts and thousands of genomes. First, fai allows the identification of orthologous instances of a query gene cluster of interest amongst a database of target genomes. Subsequently, zol enables reliable, context-specific inference of ortholog groups for individual protein-encoding genes across gene cluster instances. In addition, zol performs functional annotation and computes a variety of evolutionary statistics for each inferred ortholog group. Importantly, in comparison to tools for visual exploration of homologous relationships between gene clusters, zol can scale to thousands of gene cluster instances and produce detailed reports that are easy to digest. To showcase fai and zol, we apply them for: (i) longitudinal tracking of a virus in metagenomes, (ii) discovering novel population-level genetic insights of two common BGCs in the fungal species

Identifiers

PMID37333121
PMCPMC10274777

What OpenQuestion holds

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LicenceCC BY-ND
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.