ArticleBioinformatics (Oxford, England)2022
Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Readout of intrinsic and induced DNA shape by homeodomain transcription factor complexes.Biophysical journal · 2026Article
- Sequence-based modeling of low-affinity transcription factor-DNA binding through deep learning.NAR genomics and bioinformatics · 2026Article
- Quantitative modulation of a spatial enhancer through the biophysical properties of a transcription factor binding site.Science advances · 2026Article
- Novel fold and wing structure of Forkhead transcription factor facilitate DNA binding.Nucleic acids research · 2025Article
- Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding.Biophysical journal · 2024Article
- DNA binding specificity of all four Saccharomyces cerevisiae forkhead transcription factors.Nucleic acids research · 2023Article
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Authors and funding
3 authors.
Funding
Abstract
summarySeveral high-throughput protein-DNA binding methods currently available produce highly reproducible measurements of binding affinity at the level of the k-mer. However, understanding where a k-mer is positioned along a binding site sequence depends on alignment. Here, we present Top-Down Crawl (TDC), an ultra-rapid tool designed for the alignment of k-mer level data in a rank-dependent and position weight matrix (PWM)-independent manner. As the framework only depends on the rank of the input, the method can accept input from many types of experiments (protein binding microarray, SELEX-seq, SMiLE-seq, etc.) without the need for specialized parameterization. Measuring the performance of the alignment using multiple linear regression with 5-fold cross-validation, we find TDC to perform as well as or better than computationally expensive PWM-based methods. AVAILABILITY AND IMPLEMENTATION: TDC can be run online at https://topdowncrawl.usc.edu or locally as a python package available through pip at https://pypi.org/project/TopDownCrawl. CONTACT: SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
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