Structure and Sequence Feature Detection

This section contains links to tools for DNA structure prediction and finding regulatory sequences, the base composition, binding sites and motifs in your sequence of interest.

Found 166 links

Displaying 15 links

CRISPRFinderTool Content

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Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Finder detects this family of direct repeats found in the DNA of many bacteria and archaea.

CSTminerTool Content

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CSTminer searches for Conserved Sequence Tags (CST) in pairwise comparisons of genomic sequences. Output is a graphical map showing the location of CSTs overlayed with known Ensembl exons and ESTs. A scoring system reflects coding or non-coding potential of these conserved blocks.

CURVES+Tool Content

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Curves+ is a web server for the analysis and visualization of the helical backbone and groove parameters of nucleic acid structures.

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DBD2BSTool Content

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DBD2BS web server uses the structure of DNA binding domains (DBDs) to predict the corresponding binding sites on DNA. Queries can be specified by a PDB ID or the coordinates of a DNA-binding protein in PDB format. DBD2BS currently maintains a list of 2,176 protein-DNA complexes and 3,135 unbound structures of DNA-binding proteins collected from PDB.

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DMINDATool Content

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DMINDA: An integrated web server for DNA motif identification and analyses.

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DNABINDPROTTool Content

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DNABINDPROT web tool is designed to predict DNA-binding residues in high frequency modes by the Gaussian network method.

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DNAshapeTool Content

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DNAshape is a web server for predicting structural features of DNA in high-throughput manner on a genome-wide scale. Input is nucleotide sequence.

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eBioinformaticsResource Content

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This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3.

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