Evidence map›Paper›PMID 39729275›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2025

Annotation of RxLR Effectors in Oomycete Genomes.

Nicholas C Cauldron, Martha A Sudermann, Camilo H Parada-Rojas, Niklaus J Grünwald

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2025. 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
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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

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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

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

4 authors.

Nicholas C CauldronDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
Martha A SudermannDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
Camilo H Parada-RojasDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
Niklaus J GrünwaldHorticultural Crops Disease and Pest Management Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR, USA. nik.grunwald@usda.gov.

Funding

USDA ARS 2072-22000-041-000-DUSDA ARS grant 2021-67034-35171USDA NIFA 2023-67013-39918
6 · The paper itself

Abstract

Pathogens have evolved effector proteins to suppress host immunity and facilitate plant infections. RxLR effectors are small, secreted effector proteins with conserved RxLR and dEER amino acid motifs at the N terminus and highly variable C termini and are commonly found in oomycete species. We provide computational approaches to annotate RxLR candidate effector genes in a genome assembly in FASTA format with an available GFF file. Hidden Markov Modeling (HHM) is used in combination with regular expressions to search for RxLR and EER amino acid patterns.

Indexed as

Computational BiologyMolecular Sequence AnnotationOomycetesAmino Acid MotifsMarkov ChainsPlant DiseasesEEREffectorRxLRSignal peptide

Identifiers

PMID39729275

What OpenQuestion holds

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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.