bio-blast-searches

# BLAST Searches Run BLAST searches against NCBI databases using Biopython's Bio.Blast module. ## Required Import ```python from Bio.Blast import NCBIWWW, NCBIXML from Bio import SeqIO ``` ## BLAST Programs | Program | Query | Database | Use Case | |---------|-------|----------|----------| | `blastn` | Nucleotide | Nucleotide | DNA/RNA sequence similarity | | `blastp` | Protein | Protein | Protein sequence similarity | | `blastx` | Nucleotide | Protein | Find protein hits for DNA query | | `tblastn` | Protein | Nucleotide | Find DNA encoding protein-like | | `tblastx` | Nucleotide | Nucleotide | Translated vs translated | ## Core Function ### NCBIWWW.qblast() Submit a BLAST query to NCBI servers. ```python from Bio.Blast import NCBIWWW # Simple BLASTN search result_handle = NCBIWWW.qblast('blastn', 'nt', sequence) ``` **Key Parameters:** | Parameter | Description | Example | |-----------|-------------|---------| | `program` | BLAST program | `'blastn'`, `'blastp'` | | `database` | Target database | `'nr'`, `'nt'`, `'refseq_rna'` | | `sequence` | Query sequence | String or SeqRecord | | `entrez_query` | Limit by Entrez query | `'Homo sapiens[organism]'` | | `hitlist_size` | Max hits to return | `50` | | `expect` | E-value threshold | `0.001` | | `word_size` | Word size | `11` for blastn | | `gapcosts` | Gap penalties | `'5 2'` (open, extend) | | `format_type` | Output format | `'XML'` (default), `'Text'` | ## Common Databases **Nucleotide:** | Database | Descripti...