A new repeat-masking method enables specific detection of homologous sequences
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Summary
This paper presents a new repeat-masking method, tantan, which is motivated by the mechanisms that create simple repeats and enables accurate homology search for non-coding DNA with extreme A + T composition.
- Type
- article
- Published
- 2010-11-24
- Cited by
- 185
- References
- 21
- Access
- Open access
- OpenAlex
- https://openalex.org/W2106263380
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:2698940
Keywords
Biology, DNA, Homology (biology), Spurious relationship, Computational biology
References
- Analysis of compositionally biased regions in sequence databases.
- Biological sequence analysis
- Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases.
- A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences
- ESTIMATING THE GUMBEL SCALE PARAMETER FOR LOCAL ALIGNMENT OF RANDOM SEQUENCES BY IMPORTANCE SAMPLING WITH STOPPING TIMES
- Parameters for accurate genome alignment
- Improved tools for biological sequence comparison.
- Markov Additive Processes and Repeats in Sequences
- More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology
- Detecting microsatellites within genomes: significant variation among algorithms
- Discovering regulatory motifs in the Plasmodium genome using comparative genomics
- Modeling the percolation of annotation errors in a database of protein sequences
- Tandem repeats finder: a program to analyze DNA sequences.
- The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions
- Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii
- Post-processing long pairwise alignments
- Amino acid substitution matrices from protein blocks.
- Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes
- Markov Additive Processes and Repeats in Sequences
Cited by
- VirusSeeker, a computational pipeline for virus discovery and virome composition analysis
- Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community
- Bioinformatics tools for lncRNA research.
- Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale
- Targeted single molecule mutation detection with massively parallel sequencing
- Gentle Masking of Low-Complexity Sequences Improves Homology Search
- Searching for Repeats, as an Example of Using the Generalized Ruzzo-Tompa Algorithm to Find Optimal Subsequences with Gaps
- Transcriptional regulation of tocopherol biosynthesis in tomato
- The tobacco genome sequence and its comparison with those of tomato and potato
- Kmasker - A Tool for in silico Prediction of Single-Copy FISH Probes for the Large-Genome Species Hordeum vulgare
- The Diversification of the LIM Superclass at the Base of the Metazoa Increased Subcellular Complexity and Promoted Multicellular Specialization
- Finding Protein-Coding Genes through Human Polymorphisms
- MsDetector: toward a standard computational tool for DNA microsatellites detection
- Split-alignment of genomes finds orthologies more accurately
- Mammalian NUMT insertion is non-random
- Probabilistic approaches to alignment with tandem repeats
- Variant surface antigens of malaria parasites: functional and evolutionary insights from comparative gene family classification and analysis
- Frameshift alignment: statistics and post-genomic applications
- Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution
- Protein expansion is primarily due to indels in intrinsically disordered regions.
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