ArticleAlgorithms for molecular biology : AMB2016
Circular sequence comparison: algorithms and applications.
Article in Algorithms for molecular biology : AMB, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 8 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
8 citing papers in PubMed.
- pLAST-a tool for rapid comparison and classification of bacterial plasmid sequences.Bioinformatics (Oxford, England) · 2026Article
- Missing value replacement in strings and applications.Data mining and knowledge discovery · 2025Article
- Prediction of Circular RNA Secondary Structures and Their Targets.Advances in experimental medicine and biology · 2025Review
- Review of techniques and models used in optical chemical structure recognition in images and scanned documents.Journal of cheminformatics · 2022Review
- On the Impact of the Data Acquisition Protocol on ECG Biometric Identification.Sensors (Basel, Switzerland) · 2021Article
- Article
- libFLASM: a software library for fixed-length approximate string matching.BMC bioinformatics · 2016Article
- Erratum to: Circular sequence comparison: algorithms and applications.Algorithms for molecular biology : AMB · 2016Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSequence comparison is a fundamental step in many important tasks in bioinformatics; from phylogenetic reconstruction to the reconstruction of genomes. Traditional algorithms for measuring approximation in sequence comparison are based on the notions of distance or similarity, and are generally computed through sequence alignment techniques. As circular molecular structure is a common phenomenon in nature, a caveat of the adaptation of alignment techniques for circular sequence comparison is that they are computationally expensive, requiring from super-quadratic to cubic time in the length of the sequences.
resultsIn this paper, we introduce a new distance measure based on q-grams, and show how it can be applied effectively and computed efficiently for circular sequence comparison. Experimental results, using real DNA, RNA, and protein sequences as well as synthetic data, demonstrate orders-of-magnitude superiority of our approach in terms of efficiency, while maintaining an accuracy very competitive to the state of the art.
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.