bio-sequence-similarity
Find homologous sequences using iterative BLAST (PSI-BLAST), profile HMMs (HMMER), and reciprocal best hit analysis. Use when identifying orthologs, distant homologs, or protein family members where standard BLAST is not sensitive enough.
Profile →npx skills add majiayu000/claude-skill-registry --skill sequence-similarity --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Sequence Similarity Searches Advanced methods for finding homologous sequences beyond standard BLAST. ## PSI-BLAST (Position-Specific Iterated BLAST) Builds a position-specific scoring matrix (PSSM) through iterations to find distant homologs. ### Basic PSI-BLAST ```bash psiblast -query protein.fasta -db nr -out results.txt -num_iterations 3 ``` ### Save PSSM for Reuse ```bash psiblast -query protein.fasta -db nr \ -out results.txt \ -out_pssm pssm.asn \ -out_ascii_pssm pssm.txt \ -num_iterations 5 ``` ### Use Existing PSSM ```bash psiblast -in_pssm pssm.asn -db nr -out results.txt ``` ### Output Format ```bash psiblast -query protein.fasta -db nr \ -out results.txt \ -outfmt 6 \ -num_iterations 3 \ -inclusion_ethresh 0.001 ``` ### Key Parameters ```bash psiblast -query protein.fasta -db nr \ -num_iterations 5 \ -inclusion_ethresh 0.001 \ -evalue 0.01 \ -num_threads 8 \ -out results.txt ``` ### PSI-BLAST Parameters | Parameter | Default | Description | |-----------|---------|-------------| | -num_iterations | 1 | Number of iterations | | -inclusion_ethresh | 0.002 | E-value for PSSM inclusion | | -evalue | 10 | E-value threshold for reporting | | -num_threads | 1 | CPU threads |
- PSI-BLAST (Position-Specific Iterated BLAST)
- Basic PSI-BLAST
- Save PSSM for Reuse
- Use Existing PSSM
- Output Format
- Key Parameters
- PSI-BLAST Parameters
- HMMER for Profile Searches
- Search with Single Sequence
- Build Profile from Alignment
- Search Database with Profile
- Download Pfam Profiles
- Scan Sequence Against Pfam
- Parse HMMER Output
psiblast -query protein.fasta -db nr -out results.txt -num_iterations 3 psiblast -query protein.fasta -db nr \ psiblast -in_pssm pssm.asn -db nr -out results.txt jackhmmer -o results.txt -A aligned.sto --cpu 8 query.fasta database.fasta hmmbuild profile.hmm alignment.sto hmmsearch -o results.txt --tblout hits.tbl profile.hmm database.fasta hmmsearch -o results.txt --domtblout domains.tbl profile.hmm database.fasta wget https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz gunzip Pfam-A.hmm.gz hmmpress Pfam-A.hmm
What does the bio-sequence-similarity skill do?
Find homologous sequences using iterative BLAST (PSI-BLAST), profile HMMs (HMMER), and reciprocal best hit analysis. Use when identifying orthologs, distant homologs, or protein family members where standard BLAST is not sensitive enough.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill sequence-similarity --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.