MINER

MINER identifies and visualizes phylogenetic motifs (PMs) within multiple sequence alignments (MSAs) to map sequence fragments that preserve familial phylogeny and support prediction of protein functional sites.

Key Features:

• Phylogenetic motif identification: Detects PMs corresponding to catalytic regions, substrate-binding sites, and protein interfaces from MSAs.
• Structural visualization: Maps PMs onto protein structures to reveal spatial organization and clustering near surface loops and active site clefts despite limited sequence proximity.
• Conservation analysis: Reports PMs that are well conserved and also identifies less-conserved motifs that may be missed by conventional motif definitions.
• Evolutionary correlation: Correlates PMs with evolutionary trace results and assesses phylogenetic signal using bootstrapping to evaluate tree significance.
• Statistical assessment: Applies calculated false-positive expectations and standard motif-identification methods to quantify the reliability of identified motifs.

Scientific Applications:

• Protein functional site prediction: Uses PMs to predict functional sites within proteins by linking conserved or phylogenetically informative sequence fragments to known functional regions.
• Analysis of heterogeneous protein datasets: Applies to diverse proteins and heterogeneous datasets, including identification of PMs in partially buried prosthetic-group regions such as cytochrome P450 and succinate dehydrogenase.

Methodology:

Analyzes MSAs to detect sequence regions that conserve familial phylogeny, applies calculated false-positive expectations and standard motif-identification methods, correlates motifs with evolutionary trace results, and employs bootstrapping to assess tree significance.