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- Yang, Lin, et al. Show all 4 Authors
- Bioinformatics 2017 v.33 no.19 pp. 3003-3010
- DNA; binding capacity; binding sites; bioinformatics; computer software; data collection; genomics; microarray technology; models; nucleotide sequences; prediction; transcription factors
- ... Transcription factors (TFs) bind to specific DNA sequence motifs. Several lines of evidence suggest that TF-DNA binding is mediated in part by properties of the local DNA shape: the width of the minor groove, the relative orientations of adjacent base pairs, etc. Several methods have been developed to jointly account for DNA sequence and shape properties in predicting TF binding affinity. However, ...
- Yang, Lin, et al. Show all 6 Authors
- Bioinformatics 2016 v.32 no.8 pp. 1211-1213
- DNA; artificial intelligence; bioinformatics; computer software; genomics; models; nucleotide sequences; prediction; sequence analysis
- ... Summary: DNAshapeR predicts DNA shape features in an ultra-fast, high-throughput manner from genomic sequencing data. The package takes either nucleotide sequence or genomic coordinates as input and generates various graphical representations for visualization and further analysis. DNAshapeR further encodes DNA sequence and shape features as user-defined combinations of k-mer and DNA shape feature ...