ArticleBMC bioinformatics2008
Efficient computation of absent words in genomic sequences.
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 23 papers.
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Who cites it
23 citing papers in PubMed.
- Cell sorting based on single nucleotide variation enables characterization of mutation-dependent transcriptome and chromatin states.Nucleic acids research · 2025Article
- Enhanced expression of the myogenic factor Myocyte enhancer factor-2 in imaginal disc myoblasts activates a partial, but incomplete, muscle development program.Developmental biology · 2024Article
- kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species.Computational and structural biotechnology journal · 2024Article
- BLINCAR: a reusable bioluminescent and Cas9-based genetic toolset for repeatedly modifying wild-typemSphere · 2023Article
- Significant non-existence of sequences in genomes and proteomes.Nucleic acids research · 2021Article
- Spatial distribution of predicted transcription factor binding sites in Drosophila ChIP peaks.Mechanisms of development · 2016Article
- Absent words and the (dis)similarity analysis of DNA sequences: an experimental study.BMC research notes · 2016Article
- Nullomers and High Order Nullomers in Genomic Sequences.PloS one · 2016Article
- Three minimal sequences found in Ebola virus genomes and absent from human DNA.Bioinformatics (Oxford, England) · 2015Article
- Linear-time computation of minimal absent words using suffix array.BMC bioinformatics · 2014Article
- Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate.BMC bioinformatics · 2014Article
- Flanking sequence context-dependent transcription factor binding in early Drosophila development.BMC bioinformatics · 2013Article
- Pervasive sequence patents cover the entire human genome.Genome medicine · 2013Article
- Comparative analysis of DNA word abundances in four yeast genomes using a novel statistical background model.PloS one · 2013Article
- Insertion site preference of Mu, Tn5, and Tn7 transposons.Mobile DNA · 2012Article
- Microbial diversity in saliva of oral squamous cell carcinoma.FEMS immunology and medical microbiology · 2011Article
- Minimal absent words in prokaryotic and eukaryotic genomes.PloS one · 2011Article
- Minimal absent words in four human genome assemblies.PloS one · 2011Article
- The word landscape of the non-coding segments of the Arabidopsis thaliana genome.BMC genomics · 2009Article
- Multiplex primer prediction software for divergent targets.Nucleic acids research · 2009Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundAnalysis of sequence composition is a routine task in genome research. Organisms are characterized by their base composition, dinucleotide relative abundance, codon usage, and so on. Unique subsequences are markers of special interest in genome comparison, expression profiling, and genetic engineering. Relative to a random sequence of the same length, unique subsequences are overrepresented in real genomes. Shortest words absent from a genome have been addressed in two recent studies.
resultsWe describe a new algorithm and software for the computation of absent words. It is more efficient than previous algorithms and easier to use. It directly computes unwords without the need to specify a length estimate. Moreover, it avoids the space requirements of index structures such as suffix trees and suffix arrays. Our implementation is available as an open source package. We compute unwords of human and mouse as well as some other organisms, covering a genome size range from 109 down to 105 bp.
conclusionThe new algorithm computes absent words for the human genome in 10 minutes on standard hardware, using only 2.5 Mb of space. This enables us to perform this type of analysis not only for the largest genomes available so far, but also for the emerging pan- and meta-genome data.
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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.