ArticleBMC bioinformatics2014
Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 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
6 citing papers in PubMed.
- Single-Molecule Real-Time Sequencing of Full-Length Transcriptome and Identification of Genes Related to Male Development inPlants (Basel, Switzerland) · 2022Article
- 'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees.NAR genomics and bioinformatics · 2020Article
- Better quality score compression through sequence-based quality smoothing.BMC bioinformatics · 2019Article
- Fast comparison of genomic and meta-genomic reads with alignment-free measures based on quality values.BMC medical genomics · 2016Article
- On the comparison of regulatory sequences with multiple resolution Entropic Profiles.BMC bioinformatics · 2016Article
- Clustering of reads with alignment-free measures and quality values.Algorithms for molecular biology : AMB · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWith the advent of Next-Generation Sequencing technologies (NGS), a large amount of short read data has been generated. If a reference genome is not available, the assembly of a template sequence is usually challenging because of repeats and the short length of reads. When NGS reads cannot be mapped onto a reference genome alignment-based methods are not applicable. However it is still possible to study the evolutionary relationship of unassembled genomes based on NGS data.
resultsWe present a parameter-free alignment-free method, called Under2, based on variable-length patterns, for the direct comparison of sets of NGS reads. We define a similarity measure using variable-length patterns, as well as reverses and reverse-complements, along with their statistical and syntactical properties. We evaluate several alignment-free statistics on the comparison of NGS reads coming from simulated and real genomes. In almost all simulations our method Under2 outperforms all other statistics. The performance gain becomes more evident when real genomes are used.
conclusionThe new alignment-free statistic is highly successful in discriminating related genomes based on NGS reads data. In almost all experiments, it outperforms traditional alignment-free statistics that are based on fixed length patterns.
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.