Motif Finder
Motif Finder - Related Videos
07:55
Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
0 Views •
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
0 Views •
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
0 Views •
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
0 Views •
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
0 Views •
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 position weight matrix assigns scores to the possible residues at each position in a candidate pattern. Motif Finder can therefore recognize related sequences without requiring an exact match at every position. This scoring approach helps identify motif variants that retain a characteristic pattern profile, making it useful for detecting biologically related sites in DNA, RNA, or protein sequences.
It combines pattern matching or statistical models with evaluations of likely motif support, so matches are not judged only by their presence. Enrichment analysis asks whether a pattern occurs more often than expected in the analyzed sequences, while conservation examines whether it persists across related sequences. These assessments help prioritize recurring patterns with stronger biological support.
A motif shared across related sequences may indicate that the pattern has been retained because of biological importance. Motif Finder can compare recurrence with conservation instead of treating every match equally. This is especially useful when investigating regulatory elements, protein domains, or RNA structures, because conserved patterns provide stronger candidates for functional interpretation and comparative analysis.
Researchers provide DNA, RNA, or protein sequences according to the biological question being studied. The sequence type helps determine whether the analysis focuses on transcription-factor binding sites, regulatory elements, protein domains, or RNA structures. Matching the input sequences to the intended biological context makes the resulting motif candidates more relevant and easier to interpret.
After candidate patterns are detected, researchers can assess their statistical support, enrichment, and conservation. Promising motifs may then be related to gene regulation, molecular interactions, or other sequence features. Experimental validation can test whether a predicted association has a biological basis, allowing computational findings to generate focused hypotheses for laboratory investigation.
Comparing motifs across related sequences can reveal patterns that remain conserved despite other sequence differences. These findings help researchers study regulatory elements, protein domains, and RNA structures, while also connecting sequence variation with gene regulation, molecular interactions, or disease mechanisms. The results can guide selection of regions for deeper comparative analysis and experimental follow-up.