ArticleBMC systems biology2012
Palindromic sequence impedes sequencing-by-ligation mechanism.
Article in BMC systems biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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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.
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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
11 citing papers in PubMed, 62 citations in OpenAlex.
- The Evolution of Gene Sequencing Technologies: Unveiling Genetic Architecture of Nonsyndromic Orofacial Clefts.Genetics research · 2026Review
- Next generation plant biostimulants & genome sequencing strategies for sustainable agriculture development.Frontiers in microbiology · 2024Review
- Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria.Biology · 2022Review
- Next generation sequencing technologies to explore the diversity of germplasm resources: Achievements and trends in tomato.Computational and structural biotechnology journal · 2022Review
- Exact mapping of Illumina blind spots in theMicrobial genomics · 2021Article
- Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country.Diagnostics (Basel, Switzerland) · 2020Review
- VLSI Structures for DNA Sequencing-A Survey.Bioengineering (Basel, Switzerland) · 2020Review
- Long walk to genomics: History and current approaches to genome sequencing and assembly.Computational and structural biotechnology journal · 2020Review
- Management of Incidental Findings in the Era of Next-generation Sequencing.Current genomics · 2015Article
- An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology.Cancer informatics · 2015Review
- Next-generation sequencing as an approach to dairy starter selection.Dairy science & technologyReview
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCurrent next-generation sequencing (NGS) platforms adopt two types of sequencing mechanisms: by synthesis or by ligation. The former is employed by 454 and Solexa systems, while the latter by SOLiD system. Although the pros and cons for each sequencing mechanism have more or less been discussed in a number of occasions, the potential obstacle imposed by palindromic sequences has not yet been addressed.
methodsTo test the effect of the palindromic region on sequencing efficacy, we clonally amplified a paired-end ditag sequence composed of a 24-bp palindromic sequence flanked by a pair of tags from the E. coli genome. We used the near homogeneous fragments produced from MmeI digestion of the amplified clone to generate a sequencing library for SOLiD 5500xl sequencer.
resultsResults showed that, traditional ABI sequencers, which adopt sequencing-by-synthesis mechanism, were able to read through the palindromic region. However, SOLiD 5500xl was unable to do so. Instead, the palindromic region was read as miscellaneous random sequences. Moreover, readable tag sequence turned obscure ~2 bp prior to the palindromic region.
conclusionsTaken together, we demonstrate that SOLiD machines, which employ sequencing-by-ligation mechanism, are unable to read through the palindromic region. On the other hand, sequencing-by-synthesis sequencers had no difficulty in doing so.
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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.