the bioinformatics chat

Even though the double-stranded DNA has the famous regular helical shape, there are small variations in the geometry of the helix depending on what exact nucleotides its made of at that position.

In this episode of the bioinformatics chat, Hassan Samee talks about the role the DNA shape plays in recognition of the DNA by DNA-binding proteins, such as transcription factors. Hassan also explains how his algorithm, ShapeMF, can deduce the DNA shape motifs from the ChIP-seq data.

Links:

• A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs (Md. Abul Hassan Samee, Benoit G. Bruneau, Katherine Pollard)
• ShapeMF on GitHub
• A picture explaining some of the DNA shape features

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