Evidence map›Paper›PMID 35445164›Full record

ArticleJournal of open source software2021

Opfi: A Python package for identifying gene clusters in large genomics and metagenomics data sets.

Alexis M Hill, James R Rybarski, Kuang Hu, Ilya J Finkelstein, Claus O Wilke

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of open source software, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. Metagenomic discovery of CRISPR-associated transposons.Proceedings of the National Academy of Sciences of the United States of America · 2021
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Alexis M HillDepartment of Integrative Biology, The University of Texas at Austin, Austin, Texas 78712, USA.
James R RybarskiDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.
Kuang HuDepartment of Integrative Biology, The University of Texas at Austin, Austin, Texas 78712, USA.
Ilya J FinkelsteinDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.
Claus O WilkeDepartment of Integrative Biology, The University of Texas at Austin, Austin, Texas 78712, USA.

Funding

The biophysical basis of translational selectionR01GM088344 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI BARRICK, JEFFREY EVAN, WILKE, CLAUS O · 2009 to 2023
$3.5M
Mechanism, specificity, and design of CRISPR RNA-mediated gene regulationR01GM124141 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI FINKELSTEIN, ILYA J · 2017 to 2020
$1.2M
NIGMS NIH HHS R01 GM088344NIGMS NIH HHS R01 GM124141
6 · The paper itself

Abstract

Gene clusters are sets of co-localized, often contiguous genes that together perform specific functions, many of which are relevant to biotechnology. There is a need for software tools that can extract candidate gene clusters from vast amounts of available genomic data. Therefore, we developed Opfi: a modular pipeline for identification of arbitrary gene clusters in assembled genomic or metagenomic sequences. Opfi contains functions for annotation, de-deduplication, and visualization of putative gene clusters. It utilizes a customizable rule-based filtering approach for selection of candidate systems that adhere to user-defined criteria. Opfi is implemented in Python, and is available on the Python Package Index and on Bioconda (Grüning et al., 2018).

Identifiers

PMID35445164
PMCPMC9017871

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.