ArticleBMC bioinformatics2008
The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed, 45 citations in OpenAlex.
- Incipient genome erosion and metabolic streamlining for antibiotic production in a defensive symbiont.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- EvaluatingPeerJ · 2020Article
- IslandCafe: Compositional Anomaly and Feature Enrichment Assessment for Delineation of Genomic Islands.G3 (Bethesda, Md.) · 2019Article
- EuGI: a novel resource for studying genomic islands to facilitate horizontal gene transfer detection in eukaryotes.BMC genomics · 2018 · on this mapArticle
- SWPhylo - A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees.Evolutionary bioinformatics online · 2018Article
- Deciphering pathogenicity and antibiotic resistance islands in methicillin-resistantOpen biology · 2017Article
- Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YScientific reports · 2017Article
- Genomic Analysis ofFrontiers in microbiology · 2017Article
- Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes.Database : the journal of biological databases and curation · 2015Article
- Identification and characterization of carboxyl esterases of gill chamber-associated microbiota in the deep-sea shrimp Rimicaris exoculata by using functional metagenomics.Applied and environmental microbiology · 2015Article
- Role of the horizontal gene exchange in evolution of pathogenic Mycobacteria.BMC evolutionary biology · 2015Article
- Analysis of genomic rearrangements, horizontal gene transfer and role of plasmids in the evolution of industrial important Thermus species.BMC genomics · 2014Article
- Biochemical diversity of carboxyl esterases and lipases from Lake Arreo (Spain): a metagenomic approach.Applied and environmental microbiology · 2013Article
- High-density transcriptional initiation signals underline genomic islands in bacteria.PloS one · 2012Article
- Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED134.Applied and environmental microbiology · 2011Article
- Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01.BMC genomics · 2011Article
- PELPK1 (At5g09530) contains a unique pentapeptide repeat and is a positive regulator of germination in Arabidopsis thaliana.Plant cell reports · 2011Article
- Article
- Diversity of glycosyl hydrolases from cellulose-depleting communities enriched from casts of two earthworm species.Applied and environmental microbiology · 2010Article
- Comparative genomics of green sulfur bacteria.Photosynthesis research · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundData mining in large DNA sequences is a major challenge in microbial genomics and bioinformatics. Oligonucleotide usage (OU) patterns provide a wealth of information for large scale sequence analysis and visualization. The purpose of this research was to make OU statistical analysis available as a novel web-based tool for functional genomics and annotation. The tool is also available as a downloadable package.
resultsThe SeqWord Genome Browser (SWGB) was developed to visualize the natural compositional variation of DNA sequences. The applet is also used for identification of divergent genomic regions both in annotated sequences of bacterial chromosomes, plasmids, phages and viruses, and in raw DNA sequences prior to annotation by comparing local and global OU patterns. The applet allows fast and reliable identification of clusters of horizontally transferred genomic islands, large multi-domain genes and genes for ribosomal RNA. Within the majority of genomic fragments (also termed genomic core sequence), regions enriched with housekeeping genes, ribosomal proteins and the regions rich in pseudogenes or genetic vestiges may be contrasted.
conclusionThe SWGB applet presents a range of comprehensive OU statistical parameters calculated for a range of bacterial species, plasmids and phages. It is available on the Internet at http://www.bi.up.ac.za/SeqWord/mhhapplet.php.
Indexed as
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.