blastp

Quick Start

• Command: blastp
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/blastp
• Version: 2.17.0+
• Reference: references/help.md

When To Use This Tool

• Search protein queries against protein databases for close or moderate-distance homologs.
• Quick functional annotation or sanity-checking of predicted proteins.
• Use blastp-short for short peptides.
• Prefer psiblast when ordinary blastp is not sensitive enough for distant homologs.

Common Patterns

# 1) Standard protein homology search
blastp \
  -query proteins.fa \
  -db prot_db \
  -outfmt "6 qaccver saccver pident length evalue bitscore qcovhsp" \
  -evalue 1e-5 \
  -max_target_seqs 20 \
  -num_threads 8

# 2) Search short peptides
blastp \
  -task blastp-short \
  -query peptides.fa \
  -db prot_db \
  -outfmt 6

# 3) Use a custom scoring matrix when the biology justifies it
blastp \
  -query proteins.fa \
  -db prot_db \
  -matrix BLOSUM80 \
  -outfmt 7

Recommended Workflow

1. Make sure the query FASTA is truly protein and the target database is prot.
2. Start with a standard blastp run and inspect top hits before tuning matrices or thresholds.
3. Use tabular output for pipelines and pairwise text only for manual review.
4. Escalate to psiblast if you need iterative profile-based sensitivity.

Guardrails

• Query input must be amino-acid sequence, not nucleotide sequence.
• -db and -subject are mutually exclusive here too.
• Composition-based statistics are on by default; do not change -comp_based_stats casually.
• For reproducible filtering, set -evalue, -max_target_seqs, and -outfmt explicitly.