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Maximal homology alignment: A new method based on two-dimensional homology

https://doi.org/10.1101/593228
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Hawaiian Drosophila as an Evolutionary Model Clade: Days of Future Past
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Electrical response and function of a bitter substance receptor associated with the maxillary sensilla of the larva of the silkworm, Bombyx mori L.
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Phylogenetic variation in the primary structure of hemoglobins
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Lineage-Specific Regulation of theCiona snailGene in the Embryonic Mesoderm and Neuroectoderm
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Characterization of a Maternal T-Box Gene in Ciona intestinalis
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Minisatellite Origins in Yeast and Humans
inferredcites →https://doi.org/10.1007/bf01731581openalex-snapshot
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
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Mutation Biases and Mutation Rate Variation Around Very Short Human Microsatellites Revealed by Human–Chimpanzee–Orangutan Genomic Sequence Alignments
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A general method applicable to the search for similarities in the amino acid sequence of two proteins
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Identification of common molecular subsequences
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Break-induced replication: functions and molecular mechanism
inferredcites →https://doi.org/10.1016/j.tig.2019.01.002openalex-snapshot
Substitutions Are Boring: Some Arguments about Parallel Mutations and High Mutation Rates
inferredcites →https://doi.org/10.1016/j.ydbio.2013.03.002openalex-snapshot
A Schnurri/Mad/Medea complex attenuates the dorsal–twist gradient readout at vnd
inferredcites →https://doi.org/10.1016/s0168-9525(00)02022-9openalex-snapshot
Partners and pathways
inferredcites →https://doi.org/10.1016/s0168-9525(00)02139-9openalex-snapshot
Microsatellite mutations in the germline:
inferredcites →https://doi.org/10.1038/365274a0openalex-snapshot
Destabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA mismatch repair
inferredcites →https://doi.org/10.1038/74249openalex-snapshot
Heterogeneous mutation processes in human microsatellite DNA sequences
inferredcites →https://doi.org/10.1038/hdy.2008.49openalex-snapshot
Genome size diversity in the family Drosophilidae
inferredcites →https://doi.org/10.1038/nchembio.127openalex-snapshot
Malleable machines take shape in eukaryotic transcriptional regulation
inferredcites →https://doi.org/10.1038/ncomms1102openalex-snapshot
Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers
inferredcites →https://doi.org/10.1073/pnas.0400611101openalex-snapshot
Coordinate enhancers share common organizational features in the Drosophila genome
inferredcites →https://doi.org/10.1073/pnas.69.1.4openalex-snapshot
Matching Sequences under Deletion/Insertion Constraints
inferredcites →https://doi.org/10.1089/cmb.2008.20ttopenalex-snapshot
Non-Homologous Structured CRMs from the Ciona Genome
inferredcites →https://doi.org/10.1093/gbe/evs116openalex-snapshot
Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome
inferredcites →https://doi.org/10.1093/genetics/156.4.1913openalex-snapshot
The Population Genetics of the Origin and Divergence of the Drosophila simulans Complex Species
inferredcites →https://doi.org/10.1093/nar/gku212openalex-snapshot
Large-scale analysis of tandem repeat variability in the human genome
inferredcites →https://doi.org/10.1093/oso/9780195076912.001.0001openalex-snapshot
Progress and Prospects in Evolutionary Biology
inferredcites →https://doi.org/10.1101/299867openalex-snapshot
Genetic sequences are two-dimensional
inferredcites →https://doi.org/10.1101/cshperspect.a016410openalex-snapshot
An Overview of the Molecular Mechanisms of Recombinational DNA Repair
inferredcites →https://doi.org/10.1101/gr.122937.111openalex-snapshot
A matter of life or death: How microsatellites emerge in and vanish from the human genome
inferredcites →https://doi.org/10.1101/gr.130922.111openalex-snapshot
Genome sequencing reveals complex speciation in the Drosophila simulans clade
inferredcites →https://doi.org/10.1101/gr.1933104openalex-snapshot
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
inferredcites →https://doi.org/10.1101/gr.6554007openalex-snapshot
Sequence-based estimation of minisatellite and microsatellite repeat variability
inferredcites →https://doi.org/10.1126/science.147.3653.68openalex-snapshot
Evolving Genes and Proteins
inferredcites →https://doi.org/10.1146/annurev-genet-072610-155046openalex-snapshot
Variable Tandem Repeats Accelerate Evolution of Coding and Regulatory Sequences
inferredcites →https://doi.org/10.1146/annurev-genet-110410-132435openalex-snapshot
Double-Strand Break End Resection and Repair Pathway Choice
inferredcites →https://doi.org/10.1186/s12859-017-1665-1openalex-snapshot
Solving the master equation for Indels
inferredcites →https://doi.org/10.1371/journal.pbio.0060263openalex-snapshot
Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts
inferredcites →https://doi.org/10.1371/journal.pcbi.1000243openalex-snapshot
Malleable Machines in Transcription Regulation: The Mediator Complex
inferredcites →https://doi.org/10.1371/journal.pgen.1007075openalex-snapshot
How well do you know your mutation? Complex effects of genetic background on expressivity, complementation, and ordering of allelic effects
inferredcites →https://doi.org/10.1371/journal.pone.0002442openalex-snapshot
Estimation of Isolation Times of the Island Species in the Drosophila simulans Complex from Multilocus DNA Sequence Data
inferredcites →https://doi.org/10.1371/journal.pone.0101177openalex-snapshot
Microsatellite Repeat Instability Fuels Evolution of Embryonic Enhancers in Hawaiian Drosophila
inferredcites →https://doi.org/10.1371/journal.pone.0174253openalex-snapshot
Evolving Notch polyQ tracts reveal possible solenoid interference elements
inferredcites →https://doi.org/10.1534/g3.115.021659openalex-snapshot
The Nature, Extent, and Consequences of Genetic Variation in the opa Repeats of Notch in Drosophila
inferredcites →https://doi.org/10.1534/genetics.116.186791openalex-snapshot
Integration of Orthogonal Signaling by the Notch and Dpp Pathways in Drosophila
inferredcites →https://doi.org/10.1534/genetics.116.193359openalex-snapshot
Variability in a Short Tandem Repeat Mediates Complex Epistatic Interactions in Arabidopsis thaliana
inferredcites →https://doi.org/10.2307/2280633openalex-snapshot
Statistical Tables for Biological, Agricultural and Medical Research.
inferredcites →https://doi.org/10.5281/zenodo.10763570openalex-snapshot
Progress and Prospects in Evolutionary Biology. The Drosophila Model.
inferredcites →https://doi.org/10.7551/mitpress/2022.001.0001openalex-snapshot
Computational Molecular Biology

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inferred← citeshttps://doi.org/10.1101/2024.07.17.603925openalex-snapshot
2D representations of DNA sequence show that most transversions are misaligned nucleotides associated with replication slippage
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