blast-sequence-search

name	blast-sequence-search
description	BLAST skill for sequence similarity searching, homology detection, and database querying
allowed-tools	["Read","Write","Glob","Grep","Edit","WebFetch","WebSearch","Bash"]
metadata	{"version":"1.0","category":"bioinformatics","tags":["sequence-analysis","blast","homology","database-search"]}
graph	{"domains":["domain:bioinformatics"],"specializations":["specialization:biomedical-informatics"],"skillAreas":["skill-area:graph-algorithms","skill-area:string-matching","skill-area:data-analysis"],"workflows":["workflow:experiment-design"],"roles":["role:research-engineer","role:biomedical-engineer"]}

BLAST Sequence Search Skill

Purpose

Provide BLAST capabilities for sequence similarity searching, homology detection, and database querying across nucleotide and protein sequences.

Capabilities

• BLASTn/BLASTp/BLASTx execution
• Custom database creation and management
• E-value and alignment filtering
• Output parsing and result annotation
• Batch query processing
• Remote NCBI database queries

Usage Guidelines

• Select appropriate BLAST program for query/database type
• Set E-value thresholds based on search sensitivity needs
• Create custom databases for project-specific searches
• Parse and filter results for downstream analysis
• Consider computational resources for large searches
• Document database versions for reproducibility

Dependencies

• NCBI BLAST+
• DIAMOND
• MMseqs2

Process Integration

• Whole Genome Sequencing Pipeline (wgs-analysis-pipeline)
• Protein Structure Prediction (protein-structure-prediction)
• Shotgun Metagenomics Pipeline (shotgun-metagenomics)