Motif Analysis
Motif Analysis - Related Videos
07:55
Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
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Cited by 3 •
2011
A straight-forward and robust method to identify potential regulatory motifs in co-regulated genes is presented. SCOPE does not require any user parameters and returns motifs that represent excellent candidates for regulatory signals. The identification of such regulatory signals helps to understand the underlying biology.
14:28
Peptide-based Identification of Functional Motifs and their Binding Partners
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Cited by 2 •
2013
Techniques to dissect the mechanisms underlying the secretion of HIV-1 Nef in exosomes are described. Specific short peptides derived from Nef and protein transfection were exploited to determine the structure, function, and binding partners of Nef’s Secretion Modification Region. These procedures have general relevance in many mechanistic studies.
08:16
Identifying Caspases and their Motifs that Cleave Proteins During Influenza A Virus Infection
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Cited by 6 •
2022
Influenza A virus (IAV) infection activates the caspases that cleave host and viral proteins, which, in turn, have pro- and antiviral functions. By employing inhibitors, RNA interference, site-directed mutagenesis, and western blotting and RT-qPCR techniques, caspases in infected mammalian cells that cleave host cortactin and histone deacetylases were identified.
09:32
Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
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Cited by 6 •
2019
This article presents a detailed protocol for T4 ligation and denaturing PAGE purification of small circular DNA molecules, annealing and native PAGE analysis of circular tiles, assembling and AFM imaging of 1D and 2D DNA nanostructures, as well as agarose gel electrophoresis and centrifugation purification of finite DNA nanostructures.
08:59
High-Speed Atomic Force Microscopy Imaging of DNA Three-Point-Star Motif Self Assembly Using Photothermal Off-Resonance Tapping
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2024
Here, we show the imaging protocol for observing biomolecular interactions with photothermal off-resonance tapping (PORT), where we optimized imaging parameters, identified system limits, and investigated potential improvements in imaging three-point-star DNA motif assembly.
FAQs
A consensus sequence summarizes the most common nucleotide or amino acid at each motif position, whereas a position weight matrix records the preference for each possible residue at every position. This preserves variation within the pattern and supports more informative sequence scanning. In genetic studies, that added detail can improve predictions of potential transcription-factor binding sites.
Conservation provides evidence that a recurring sequence pattern may be maintained because it contributes to molecular function. Motif analysis can therefore compare sequences to identify patterns preserved across related examples, then use those patterns to characterize regulatory regions. Conserved motifs are useful candidates for further investigation, but their predicted roles still require experimental validation.
A genetic variant can change one or more positions within a sequence pattern, altering how closely the sequence matches a recognized motif. Motif analysis can compare the reference and altered sequences to identify potential changes in transcription-factor binding-site predictions. This offers a computational way to investigate variants that may influence gene regulation and inherited traits.
A typical workflow begins by selecting DNA, RNA, or protein sequences and deciding whether aligned or unaligned input is appropriate. Computational tools then scan the sequences for recurring patterns, which can be summarized with consensus sequences or position weight matrices. Researchers interpret conserved or regulatory-region motifs and use the resulting predictions to prioritize experimental validation.
Motif analysis is especially useful when researchers want to examine whether promoters or enhancers contain sequence patterns associated with transcription-factor binding. Scanning these regulatory regions can reveal candidate motifs and help connect sequence features with gene-control mechanisms. The findings can support studies of development, disease, and inherited traits by identifying regulatory sequences for subsequent testing.
In genetics, the method helps connect sequence patterns with possible biological functions and regulatory mechanisms. Researchers can use it to assess sequence conservation, predict transcription-factor binding sites, and examine whether variants might modify those predictions. These computational results do not by themselves establish function, but they can guide experiments focused on development, disease, or inherited traits.