prof_sim

prof_sim performs profile-profile comparisons of PSI-BLAST-generated protein sequence profiles to assign statistical similarity scores for detecting weak similarities and distant homologs.

Key Features:

• Profile comparison: Compares input profiles generated by PSI-BLAST using profile-profile comparison to detect statistical similarities between protein families.
• Statistical scoring: Assigns similarity scores that statistically assess the relationship between two input profiles.
• Gap-aware alignment: Accommodates gaps in the alignment process when comparing profiles.
• Alignment optimization: Produces alignments optimized to closely match structural alignments.
• Structural correlation: Alignments correlate with similarities in secondary structure elements and tertiary structures.
• Sensitivity to distant homologies: Demonstrates superior sensitivity relative to profile-based search programs such as PSI-BLAST and IMPALA for detecting distant homologous relationships.

Scientific Applications:

• Distant homology detection: Detects weak similarities within the "twilight zone" of sequence similarity to uncover distant homologs.
• Evolutionary biology: Supports studies of protein family relationships and evolutionary inference.
• Protein function prediction: Aids prediction of protein function through detection of remote homologs.
• Structural genomics and proteomics: Assists structural genomics and proteomics research by producing alignments correlated with structural elements.

Methodology:

Compares PSI-BLAST-generated profiles via profile-profile comparison, assigns statistical similarity scores, accommodates gaps in alignments, and optimizes alignments to match structural alignments.