ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2011
Species-specific typing of DNA based on palindrome frequency patterns.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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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.
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Who cites it
5 citing papers in PubMed, 13 citations in OpenAlex.
- DNA Materials Assembled from One DNA Strand.International journal of molecular sciences · 2023Review
- Palindromic Vectors, Symmetropy and Symmentropy as Symmetry Descriptors of Binary Data.Entropy (Basel, Switzerland) · 2022Article
- Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots.Frontiers in genetics · 2013Article
- A base composition analysis of natural patterns for the preprocessing of metagenome sequences.BMC bioinformatics · 2013Article
- The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2012Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA in its natural, double-stranded form may contain palindromes, sequences which read the same from either side because they are identical to their reverse complement on the sister strand. Short palindromes are underrepresented in all kinds of genomes. The frequency distribution of short palindromes exhibits more than twice the inter-species variance of non-palindromic sequences, which renders palindromes optimally suited for the typing of DNA. Here, we show that based on palindrome frequency, DNA sequences can be discriminated to the level of species of origin. By plotting the ratios of actual occurrence to expectancy, we generate palindrome frequency patterns that allow to cluster different sequences of the same genome and to assign plasmids, and in some cases even viruses to their respective host genomes. This finding will be of use in the growing field of metagenomics.
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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.