domains / families / data / remote-homology

remote-homology

separate

Detect distant homologs using profile and structure-aware methods that go beyond standard BLAST. Use when sequence identity falls into the twilight zone (<35% pairwise), when BLAST fails to find homologs that should exist, when working at metagenomic scale (DIAMOND, MMseqs2), or when structure beats sequence (Foldseek). Covers PSI-BLAST (iterative PSSM), jackhmmer (iterative HMM), HHblits/HHsearch (profile-profile), DIAMOND, MMseqs2, and Foldseek (3Di structural alphabet, van Kempen 2024).

When to use

• Detect distant homologs
• Sequence identity <35% pairwise
• BLAST fails to find homologs
• Metagenomic scale workflows
• Structure-aware homology search
• PSI-BLAST iterative PSSM
• jackhmmer iterative HMM
• HHblits/HHsearch profile-profile

When not to use

• Standard BLAST detection above 35% identity

Skill page

Source