ArticleBioinformatics advances2024
Marker discovery in the large.
Article in Bioinformatics advances, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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Who cites it
4 citing papers in PubMed.
- SURE-Pipe: a pipeline to compare genomes and extract shared and unique regions.NAR genomics and bioinformatics · 2026Article
- Seqwin: ultrafast identification of signature sequences in microbial genomes.Bioinformatics (Oxford, England) · 2026Article
- Seqwin: Ultrafast identification of signature sequences in microbial genomes.bioRxiv : the preprint server for biology · 2025Article
- Fast detection of unique genomic regions.Computational and structural biotechnology journal · 2025Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: Markers for diagnostic polymerase chain reactions are routinely constructed by taking regions common to the genomes of a target organism and subtracting the regions found in the targets' closest relatives, their neighbors. This approach is implemented in the published package Fur, which originally required memory proportional to the number of nucleotides in the neighborhood. This does not scale well. Results: Here, we describe a new version of Fur that only requires memory proportional to the longest neighbor. In spite of its greater memory efficiency, the new Fur remains fast and is accurate. We demonstrate this by applying it to simulated sequences and comparing it to an efficient alternative. Then we use the new Fur to extract markers from 120 reference bacteria. To make this feasible, we also introduce software for automatically finding target and neighbor genomes and for assessing markers. We pick the best primers from the 10 most sequenced reference bacteria and show their excellent Availability and implementation: Fur is available from github.com/evolbioinf/fur, in the Docker image hub.docker.com/r/beatrizvm/mapro, and in the Code Ocean capsule 10.24433/CO.7955947.v1.
Identifiers
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Registered trials
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.