ReviewGenomics, proteomics & bioinformatics2015
A brief review of software tools for pangenomics.
Review in Genomics, proteomics & bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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.
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.
Who cites it
25 citing papers in PubMed.
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Adding context to the pneumococcal core genes using bioinformatic analysis of the intergenic pangenome ofFrontiers in bioinformatics · 2023Article
- Review
- Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook.Briefings in bioinformatics · 2021Article
- From genomes to molecular dynamics - A bottom up approach in extrication of SARS CoV-2 main protease inhibitors.Computational toxicology (Amsterdam, Netherlands) · 2021Article
- High-Throughput Genotyping Technologies in Plant Taxonomy.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Integrating pan-genome with metagenome for microbial community profiling.Computational and structural biotechnology journal · 2021Review
- Pan-genome: A promising resource for noncoding RNA discovery in plants.The plant genome · 2020Review
- Pan- and core- gene association networks: Integrative approaches to understanding biological regulation.PloS one · 2019Article
- Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost.BMC genomics · 2018Article
- No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects.Microbial biotechnology · 2018Review
- PGAP-X: extension on pan-genome analysis pipeline.BMC genomics · 2018Article
- Computational pan-genomics: status, promises and challenges.Briefings in bioinformatics · 2018Review
- PGAweb: A Web Server for Bacterial Pan-Genome Analysis.Frontiers in microbiology · 2018Article
- Genome Sequencing and Pan-Genome Analysis of 23Frontiers in microbiology · 2018Article
- KinFin: Software for Taxon-Aware Analysis of Clustered Protein Sequences.G3 (Bethesda, Md.) · 2017Article
- Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species.Frontiers in plant science · 2017Article
- PanWeb: A web interface for pan-genomic analysis.PloS one · 2017Article
- New Tools in Orthology Analysis: A Brief Review of Promising Perspectives.Frontiers in genetics · 2017Review
- Corrected Genome Annotations Reveal Gene Loss and Antibiotic Resistance as Drivers in the Fitness Evolution of Salmonella enterica Serovar Typhimurium.Journal of bacteriology · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis. By the end of 2014, Panseq and the pan-genomes analysis pipeline (PGAP) ranked as the top two most popular packages according to cumulative citations of peer-reviewed scientific publications. The functions of the software packages and tools, albeit variable among them, include categorizing orthologous genes, calculating pangenomic profiles, integrating gene annotations, and constructing phylogenies. As epigenomic elements are being gradually revealed in prokaryotes, it is expected that pangenomic databases and toolkits have to be extended to handle information of detailed functional annotations for genes and non-protein-coding sequences including non-coding RNAs, insertion elements, and conserved structural elements. To develop better bioinformatic tools, user feedback and integration of novel features are both of essence.
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Identifiers
What OpenQuestion holds
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.