3MATRIX visualizes the three dimensional structure of eMATRIX motifs contained within structures from the Protein Structure Database (PDB). One needs the Chime plug-in to view the 3MATRIX motif structures. Multiple views of the structural motifs are possible.
3MOTIF visualizes the three dimensional structure of eMOTIFs contained within structures from the Protein Structure Database (PDB). One needs the Chime plug-in to view the 3MOTIF structures. Multiple views of the structural motifs are possible.
(1) eMOTIF-SEARCH: Given a protein sequence, the eMOTIF-SEARCH program suggests families of proteins to which the query sequence may belong. The eMOTIF-SEARCH program considers a protein sequence a potential member of a protein family, if the sequence contains discrete motif or motifs that have been generated from an ungapped multiple sequence alignment of known member sequences from that family.
(2) eMOTIF-MAKER: The eMOTIF-MAKER program converts an ungapped multiple sequence alignment into a set of Pareto-optimal discrete motifs for use by the eMOTIF-SEARCH program and the eMOTIF-SCAN program. The resulting set of motifs often reveals sub-families within the cluster of proteins that share the region of sequence similarity covered by the given ungapped multiple sequence alignment.
(3) eMOTIF-SCAN: Given a regular expression, the eMOTIF-SCAN program finds all the occurrences of that regular expression in a particular sequence database.
MOTIFREGRESSOR for discovering sequence motifs upstream of genes that undergo expression changes in a given condition. The method combines the advantages of matrix-based motif finding and oligomer motif-expression regression analysis, resulting in high sensitivity and specificity. MOTIF REGRESSOR is particularly effective in discovering expression-mediating motifs of medium to long width with multiple degenerate positions.
MDScan (Motif Discovery scan) discovers conserved transcription factor binding sites among upstream sequences from chromatin immune precipitation experiments (CHIP) as well as from single microarray experiments. The algorithm is strictly deterministic, not discovering local minima and always giving the globally best conserved motif. It is faster than most other algorithms and nearly as sensitive as BioProspector.
LocalMotif is a software tool for discovering transcription factor binding motifs in a collection of DNA sequences. LocalMotif is based on a novel scoring function, called spatial confinement score, which can determine the exact interval of localization of a motif. This score is combined with other existing scoring measures including over-representation and relative entropy to determine the overall prominence of the motif. The approach successfully discovers biologically relevant motifs and their intervals of localization in scenarios where the motifs cannot be discovered by general motif finding tools. It is especially useful for discovering multiple co-localized motifs in a set of regulatory sequences, such as those identified by ChIP-Seq.