Evidence map›Paper›PMID 38172704›Full record

ArticleBMC genomics2024

A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences.

Anton Frisgaard Nørrevang, Sergey Shabala, Michael Palmgren

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 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, top 100% of its field
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, 0 citations in OpenAlex.

No citing paper in PubMed yet.

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

3 authors at 2 institutions in 3 countries.

Anton Frisgaard NørrevangNovoCrops Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, DK-1871, Denmark.
Sergey ShabalaSchool of Biological Sciences, University of Western Australia, Crawley, WA6009, Australia.
Michael PalmgrenNovoCrops Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, DK-1871, Denmark. palmgren@plen.ku.dk.
University of Copenhagen · DKThe University of Western Australia · AU

Funding

Carlsbergfondet RaisingQuinoaNovo Nordisk Fonden NovoCrops
6 · The paper itself

Abstract

Databases of genome sequences are growing exponentially, but, in some cases, assembly is incomplete and genes are poorly annotated. For evolutionary studies, it is important to identify all members of a given gene family in a genome. We developed a method for identifying most, if not all, members of a gene family from raw genomes in which assembly is of low quality, using the P-type ATPase superfamily as an example. The method is based on the translation of an entire genome in all six reading frames and the co-occurrence of two family-specific sequence motifs that are in close proximity to each other. To test the method's usability, we first used it to identify P-type ATPase members in the high-quality annotated genome of barley (Hordeum vulgare). Subsequently, after successfully identifying plasma membrane H

Indexed as

HordeumP-type ATPasesAdenosine TriphosphatasesGenome, PlantPhylogenyAdenosine TriphosphatasesP-type ATPasesFragmented genomesGene familiesHalophytesPlasma membrane H+-ATPaseP-type ATPaseTwo-motif

Identifiers

PMID38172704
PMCPMC10763278
OpenAlexW4390544211

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.