FISH - sequence search

FISH - sequence search identifies the family membership of protein domains within query sequences by integrating sequence and structural information using structure-anchored Hidden Markov Models (saHMMs).

Key Features:

• High Accuracy: Achieves a 99.3% top-hit family assignment success rate on SCOP sequences at an E-value cutoff of 0.1.
• Structure-Anchored Hidden Markov Models (saHMMs): Employs saHMMs that integrate sequence and structural information to detect domains with low sequence similarity to known proteins.
• Functional Annotation: Provides functional annotations for identified domain families to suggest potential roles within proteins.
• Structural Predictions: Produces probable 2D and 3D structural predictions for identified domains to inform protein architecture and function analyses.
• Sequence Alignments: Generates pairwise and multiple sequence alignments with low-identity homologues to support comparative and evolutionary analyses.
• Custom Searches: Supports analysis of user-supplied protein sequences and searches of public sequence databases using individual saHMMs.

Scientific Applications:

• Protein Function Prediction: Identifies domain families and associated annotations to aid prediction of functions for uncharacterized proteins.
• Structural Biology: Provides structural predictions to support studies of protein folding, stability, and interaction networks.
• Comparative Genomics: Produces low-identity sequence alignments enabling evolutionary comparisons and analysis of conserved domain architectures across species.

Methodology:

Leverages structure-anchored Hidden Markov Models to integrate sequence and structural information for robust identification of protein domain families.